Waters in room temperature and cryo protein crystal structures

2016 ◽  
Vol 231 (11) ◽  
Author(s):  
Oliviero Carugo
Keyword(s):  
Low Temperature ◽  
Crystal Structures ◽  
Room Temperature ◽  
Protein Structures ◽  
Water Structure ◽  
Protein Crystal ◽  
Quality Data ◽  
Water Molecules ◽  
Data Sets ◽  
Density Maps

AbstractSince it has been observed that low temperature protein crystal structures may differ from room temperature structures, it is necessary to compare systematically the protein hydration structure in low and room protein crystal structures. High quality data sets of protein structures were built in an extremely rigorous manner and crystal symmetry was included in the identification of four types of water molecules (buried in the protein core, deeply inserted into crevices at the protein surface, first and second hydration layers). More water molecules are observed at low temperature only if the resolution is better than 2.1–2.3 Å. At worse resolution, temperature does not play any role. The numerous water molecules that become detectable at low temperature and at higher resolution are more mobile, relative to the protein average flexibility. Despite that, the occupancy does not depend on temperature. It can be hypothesized that water structure and around proteins and hydrogen bond network do not depend on the temperature, at least in the temperature range examined here. At low temperature more water molecules are detected because the average flexibility of all the atoms decreases, so that also water molecules that are considerably more mobile than the average atoms become observable in the electron density maps.

Removing bias from solvent atoms in electron density maps

2008 ◽  
Vol 41 (4) ◽  
pp. 761-767 ◽  
Author(s):  
Eric N. Brown
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Protein Crystal ◽  
Water Molecules ◽  
Data Set ◽  
Atomic Structures ◽  
Research Article ◽  
Density Maps ◽  
Atom Position

Atomic structures of proteins determinedviaprotein crystallography contain numerous solvent atoms. The experimental data for the determination of a water molecule's O-atom position is often a small contained blob of unidentified electron density. Unfortunately, the nature of crystallographic refinement lets poorly placed solvent atoms bias the future refined positions of all atoms in the crystal structure. This research article presents the technique of omit-maps applied to remove the bias introduced by poorly determined solvent atoms, enabling the identification of incorrectly placed water molecules in partially refined crystal structures. A total of 160 protein crystal structures with 45 912 distinct water molecules were processed using this technique. Most of the water molecules in the deposited structures were well justified. However, a few of the solvent atoms in this test data set changed appreciably in position, displacement parameter or electron density when fitted to the solvent omit-map, raising questions about how much experimental support exists for these solvent atoms.

scholarly journals Radiation damage effects on protein conformation at room temperature and 100K

2014 ◽  
Vol 70 (a1) ◽  
pp. C344-C344
Author(s):  
Silvia Russi ◽  
Shawn Kann ◽  
Henry van den Bedem ◽  
Ana M. González
Keyword(s):  
Data Collection ◽  
Radiation Damage ◽  
Crystal Structures ◽  
Room Temperature ◽  
Relative Rate ◽  
Absorbed Dose ◽  
Conformational Ensemble ◽  
Data Sets ◽  
Cryogenic Temperatures ◽  
Full Data

Protein crystallography data collection at synchrotrons today is routinely carried out at cryogenic temperatures to mitigate radiation damage to the crystal. Although damage still takes place, at 100 K and below, the immobilization of free radicals increases the lifetime of the crystals by orders of magnitude. Increasingly, experiments are carried out at room temperature. The lack of adequate cryo-protectants, the induced lattice changes or internal disorders during the cooling process, and the convenience of collecting data directly from the crystallization plates, are some of the reasons. Moreover, recent studies have shown that flash-freezing affects the conformational ensemble of crystal structures [1], and can hide important functional mechanisms from observation [2]. While there has been a considerable amount of effort in studying radiation damage at cryo-temperatures, its effects at room temperature are still not well understood. We investigated the effects of data collection temperature on secondary local damage to the side chain and main chain from different proteins. Data were collected from crystals of thaumatin and lysozyme at 100 K and room temperature. To carefully control the total absorbed dose, full data sets at room temperature were assembled from a few diffraction images per crystal. Several data sets were collected at increasing levels of absorbed dose. Our analysis shows that while at cryogenic temperatures, radiation damage increases the conformational variability, _x0004_at room temperature it has the opposite effect_x0005_. We also observed that disulfide bonds appear to break up at a different relative rate at room temperature, perhaps because of a more active repair mechanism. Our analysis suggests that elevated conformational heterogeneity in crystal structures at room temperature is observed despite radiation damage, and not as a result thereof.

Crystal Structures of Piperazinium Tetrabromocadmate(II)-Monohydrate [C4H12N2]CdBr4 · H2O, PiperaziniumTetraiodocadmate(II) [C4H12N2]CdI4, and Bis(trimethylsulphonium) Tetrabromocadmate(II) [(CH3)3S]2CdBr4

2002 ◽  
Vol 57 (5) ◽  
pp. 503-508 ◽  
Author(s):  
Hideta Ishihara ◽  
Keizo Horiuchi ◽  
Thorsten M. Gesing ◽  
Shi-qi Dou ◽  
J.-Christian Buhl ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Room Temperature ◽  
Water Molecules ◽  
Temperature Phase

Piperazinium tetrabromocadmate(II)-monohydrate, [C4H12N2]CdBr4 · H2O (1) crystallizes with isolated [CdBr4]2- anions, piperazinium cations, and water molecules (monoclinic, P21/c, Z = 4, a = 698.7(1), b = 1348.6(3), and c = 1432.4(3) pm, β = 92.97(3)˚ at 293 K). The crystal structure of 1 is almost the same as that reported in Inorg. Chim. Acta 187, 141 (1991). The crystal of piperazinium tetraiodocadmate(II), [C4H14N2]CdI4 (2) consists of isolated [CdI4]2- anions and piperazinium cations (orthorhombic,P212121, Z=4, a = 903.2(5), b = 1226.3(6), and c = 1307.9(7) pm at 293 K). The room temperature phase of bis(trimethylsulphonium) tetrabromocadmate( II), [(CH3)3S]2CdBr4 (3) has isolated [CdBr4]2- anions and trimethylsulphonium cations (orthorhombic, P212121, Z = 4, a = 911.3(1), b = 1329.2(2), and c = 1454.7(2) pm at 293 K).

scholarly journals Old structures revisited: Better insights from new data

2014 ◽  
Vol 70 (a1) ◽  
pp. C1692-C1692
Author(s):  
Graciela Díaz de Delgado ◽  
Belkis Ramírez V. ◽  
William Velásquez ◽  
Julio Trejo Dávila ◽  
Chun-Hsing Chen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Data Collection ◽  
Diffuse Scattering ◽  
Room Temperature ◽  
Structural Features ◽  
Quality Data ◽  
Unit Cell Parameters ◽  
Cell Parameters ◽  
Maleamic Acid ◽  
Monoclinic Cell

The need for improving the description of structural features with better quality data, at low temperature and with modern 2D detectors of certain materials, sometimes leads to surprisingly new insights into a previously reported structure. When attempting to grow single crystals of maleamic acid, good crystals of ammonium maleate, NH4(Mal), were obtained. Although the structure of this material has been reported at room temperature, in space group Pbcm with V=613.2(5) Å3[1], synchrotron data were collected at low temperature to examine the behavior of the ammonium moiety. The data collected lead to a structure better described in Pbca, a=8.9687(12), b=8.1604(8), c=16.348(2) Å, V=1196.5(2) Å3, Z=8. The refinement converged to R=0.0438, wR2=0.1156, S=1.02. An examination of the new data indicates that reflections with h odd are systematically weak but, nevertheless, present. The Ca derivative of valproic acid (a common anticonvulsant) was reported as monoclinic, C2/c, with a=16.250(8), b=18.471(17), c=7.729(7) Å, β=109.71(5)0, V=2183.97 Å3, Z=4, and R=10.94% [2]. However, data collection at room temperature and under a stream of nitrogen on several newly prepared crystals always lead to a triclinic, P-1 cell, with approximately half the volume of the reported cell. Attempts to index the dataset using the known monoclinic cell resulted in high uncertainties for the unit cell parameters and high Rint values since reflection spots showed splitting and diffuse scattering. The new cell had dimensions a=7.6995(4) Å, b=11.7444(6) Å, c=11.7708(6) Å, α=91.089(3)0, β=101.643(3)0, γ=102.041(3)0, V=1017.47(99) Å3, Z=2. Although the initial refinement was discouraging (R=0.1172, wR2=0.360, S=1.12) the analysis with PLATON indicated the presence of twining and, after considering the twin law, the refinement improved significantly (R=0.059, wR2=0.1472, S=0.99). Several examples where a new data collection resulted in interesting results will be presented.

Protein phasing at non-atomic resolution by combining Patterson andVLDtechniques

2014 ◽  
Vol 70 (7) ◽  
pp. 1994-2006 ◽  
Author(s):  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Giuliana Comunale ◽  
Carmelo Giacovazzo ◽  
...  
Keyword(s):  
Model Building ◽  
Protein Structures ◽  
Experimental Information ◽  
Atomic Resolution ◽  
Data Sets ◽  
Density Maps ◽  
Combined Use ◽  
Final Electron ◽  
Automatic Model Building

Phasing proteins at non-atomic resolution is still a challenge for anyab initiomethod. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (Cmap), theVLD(vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and thefree lunchextrapolation method] have been combined to overcome the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from atomic to 2.1 Å, with the condition that S or heavier atoms are present in the protein structure. The applications include the use ofARP/wARPto check the quality of the final electron-density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, but also suggest that the solution of protein structures at 2.1 Å resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures:e.g.the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version ofSIR2014.

Phase Transitions and Water Dynamics of [Mn(H2O)6](ClO4 )2 Studied by Differential Scanning Calorimetry and Neutron Scattering Methods

2000 ◽  
Vol 55 (9-10) ◽  
pp. 759-764 ◽  
Author(s):  
E. Mikuli ◽  
A. Migdał-Mikuli ◽  
I. Natkaniec ◽  
J. Mayer
Keyword(s):  
Phase Transition ◽  
Low Temperature ◽  
Neutron Scattering ◽  
Structural Phase Transition ◽  
Room Temperature ◽  
Structural Phase ◽  
Water Dynamics ◽  
Water Molecules ◽  
Temperature Phase ◽  
Solid Phases

Abstract DSC measurements performed at 95 -290 K have shown that [Mn(H 2 O) 6 ](CIO 4) 2 possesses, besides a high-temperature phase, existing above 323 K, four low-temperature solid phases. The inelastic incoherent neutron scattering (IINS) spectra and neutron powder diffraction (NPD) pat-terns registered at 20 -290 K have supported the DSC results and provided evidence that the investigated substance possesses even more than five solid phases. The IINS spectra have shown that in the room-temperature phase, water molecules perform fast stochastic reorientation at the picosecond scale. The orientational disorder characteristic for the room-temperature phase can be easily overcooled and frozen. Even by relatively slow cooling at ca. 40 K/hour a metastable, orientational (protonic) glass phase is formed below ca. 160 K. Below ca. 100 K, a structural phase transition was observed by the NPD, however the IINS spectra indicate existence of the pure ordered low-temperature phase only after annealing the sample for a few hours at 100 K. On heating, a structural phase transition takes place at ca. 120 K, and at ca. 225 K water molecules begin fast reorientation.

How many water molecules can be detected by protein crystallography?

1999 ◽  
Vol 55 (2) ◽  
pp. 479-483 ◽  
Author(s):  
Oliviero Carugo ◽  
Domenico Bordo
Keyword(s):  
Room Temperature ◽  
Protein Crystallography ◽  
Protein Crystal ◽  
Expected Improvement ◽  
Water Molecules ◽  
Asymmetric Unit ◽  
Protein Crystal Structure ◽  
Protein Models ◽  
Crystal Volume

The number of water molecules which are expected to be experimentally located by protein crystallography was determined by multiple regression analysis on a test set of 873 known protein crystal structures determined at room temperature and on another set of 33 structures determined at low temperature. The dependence of the number of water molecules included in the protein models as a function of a number of significant regressors, such as resolution, fraction of crystal volume occupied by the solvent, number of residues in the asymmetric unit, fraction of apolar protein surface or secondary structure, has been studied. The number of water molecules included in crystallographic models depends primarily on the resolution at which the structure has been solved, while the temperature of the data collection has only marginal influence. On average, at 2.0 Å resolution one water molecule per residue is included in the model, while at 1.0 Å resolution about 1.6–1.7 are crystallographically located. At 2.0 Å resolution the well known rule-of-thumb of `one water per protein residue' is confirmed, though the number of water molecules experimentally observed is strongly dependent on resolution. The results presented are useful in assessing the quality of a protein crystal structure, in selecting structural results to be compared and in evaluating the expected improvement on the solvent structure when increasing the crystallographic resolution.

scholarly journals Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis

2019 ◽  
Author(s):  
Helena W. Qi ◽  
Heather Kulik
Keyword(s):  
Amino Acids ◽  
High Resolution ◽  
Crystal Structures ◽  
Close Contact ◽  
Protein Structures ◽  
Protein Crystal ◽  
X Ray ◽  
High Quality Protein ◽  
Van Der Waals Radii ◽  
Close Contacts

<div><div><div><p>We investigate unexpectedly short non-covalent distances (< 85% of the sum of van der Waals radii) in atomically resolved X-ray crystal structures of proteins. We curate over 13,000 high quality protein crystal structures and an ultra-high resolution (1.2 Å or better) subset containing > 1,000 structures. Although our non-covalent distance criterion excludes standard hydrogen bonds known to be essential in protein stability, we observe over 82,000 close contacts in the curated protein structures. Analysis of the frequency of amino acids participating in these interactions demonstrates some expected trends (i.e., enrichment of charged Lys, Arg, Asp, and Glu) but also reveals unexpected enhancement of Tyr in such interactions. Nearly all amino acids are observed to form at least one close contact with all other amino acids, and most interactions are preserved in the much smaller ultra high-resolution subset. We quantum-mechanically characterize the interaction energetics of a subset of > 6,000 close contacts with symmetry adapted perturbation theory to enable decomposition of interactions. We observe the majority of close contacts to be favorable. The shortest favorable non-covalent distances are under 2.2 Å and are very repulsive when characterized with classical force fields. This analysis reveals stabilization by a combination of electrostatic and charge transfer effects between hydrophobic (i.e., Val, Ile, Leu) amino acids and charged Asp or Glu. We also observe a unique hydrogen bonding configuration between Tyr and Asn/Gln involving both residues acting simultaneously as hydrogen bond donors and acceptors. This work confirms the importance of first-principles simulation in explaining unexpected geometries in protein crystal structures.</p></div></div></div>

scholarly journals (NH4)Mg(HSO4)(SO4)(H2O)2 and NaSc(CrO4)2(H2O)2, two crystal structures comprising kröhnkite-type chains, and the temperature-induced phase transition (NH4)Mg(HSO4)(SO4)(H2O)2\rightleftharpoons (NH4)MgH(SO4)2(H2O)2

2021 ◽  
Vol 77 (3) ◽  
pp. 144-151
Author(s):  
Matthias Weil ◽  
Uwe Kolitsch
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Room Temperature ◽  
Classification Scheme ◽  
Three Dimensional ◽  
Structure Type ◽  
Group Symmetry ◽  
Water Molecules

The crystal structure of the mineral kröhnkite, Na2Cu(SO4)2(H2O)2, contains infinite chains composed of [CuO4(OH2)2] octahedra corner-linked with SO4 tetrahedra. Such or similar tetrahedral–octahedral `kröhnkite-type' chains are present in the crystal structures of numerous compounds with the composition AnM(XO4)2(H2O)2. The title compounds, (NH4)Mg(HSO4)(SO4)(H2O)2, ammonium magnesium hydrogen sulfate sulfate dihydrate, and NaSc(CrO4)2(H2O)2, sodium scandium bis(chromate) dihydrate, are members of the large family with such kröhnkite-type chains. At 100 K, (NH4)Mg(HSO4)(SO4)(H2O)2 has an unprecedented triclinic crystal structure and contains [MgO4(OH2)2] octahedra linked by SO3(OH) and SO4 tetrahedra into chains extending parallel to [\overline{1}10]. Adjacent chains are linked by very strong hydrogen bonds between SO3(OH) and SO4 tetrahedra into layers parallel to (111). Ammonium cations and water molecules connect adjacent layers through hydrogen-bonding interactions of medium-to-weak strength into a three-dimensional network. (NH4)Mg(HSO4)(SO4)(H2O)2 shows a reversible phase transition and crystallizes at room temperature in structure type E in the classification scheme for structures with kröhnkite-type chains, with half of the unit-cell volume for the resulting triclinic cell, and with disordered H atoms of the ammonium tetrahedron and the H atom between two symmetry-related sulfate groups. IR spectroscopic room-temperature data for the latter phase are provided. Monoclinic NaSc(CrO4)2(H2O)2 adopts structure type F1 in the classification scheme for structures with kröhnkite-type chains. Here, [ScO4(OH2)2] octahedra (point group symmetry \overline{1}) are linked by CrO4 tetrahedra into chains parallel to [010]. The Na+ cations (site symmetry 2) have a [6 + 2] coordination and connect adjacent chains into a three-dimensional framework that is consolidated by medium–strong hydrogen bonds involving the water molecules. Quantitative structural comparisons are made between NaSc(CrO4)2(H2O)2 and its isotypic NaM(CrO4)2(H2O)2 (M = Al and Fe) analogues.

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