scholarly journals A comparative anatomy of protein crystals: lessons from the automatic processing of 56,000 samples

2019 ◽  
Author(s):  
Olof Svensson ◽  
Maciej Gilski ◽  
Didier Nurizzo ◽  
Matthew W. Bowler
Keyword(s):  
Molecular Weight ◽  
Data Collection ◽  
Comparative Anatomy ◽  
Automatic Processing ◽  
Data Set ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystal Volume

SynopsisThe automatic processing of over 56,000 crystals by the autonomous ESRF beamline MASSIF-1 has provided a data set of crystal characteristics and properties that allows many theoretical proposals and assumptions to be evaluated experimentally.AbstractThe fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving the sample location, characterisation and data collection algorithms. After operating for four years, MASSIF-1 has now processed over 56,000 samples, gathering information at each stage, from the volume of the crystal to the unit cell dimensions, space group, quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals and intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.

scholarly journals A comparative anatomy of protein crystals: lessons from the automatic processing of 56 000 samples

IUCrJ ◽  
2019 ◽  
Vol 6 (5) ◽  
pp. 822-831 ◽  
Author(s):  
Olof Svensson ◽  
Maciej Gilski ◽  
Didier Nurizzo ◽  
Matthew W. Bowler
Keyword(s):  
Molecular Weight ◽  
Data Collection ◽  
Comparative Anatomy ◽  
Automatic Processing ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystal Volume ◽  
Made In

The fully automatic processing of crystals of macromolecules has presented a unique opportunity to gather information on the samples that is not usually recorded. This has proved invaluable in improving sample-location, characterization and data-collection algorithms. After operating for four years, MASSIF-1 has now processed over 56 000 samples, gathering information at each stage, from the volume of the crystal to the unit-cell dimensions, the space group, the quality of the data collected and the reasoning behind the decisions made in data collection. This provides an unprecedented opportunity to analyse these data together, providing a detailed landscape of macromolecular crystals, intimate details of their contents and, importantly, how the two are related. The data show that mosaic spread is unrelated to the size or shape of crystals and demonstrate experimentally that diffraction intensities scale in proportion to crystal volume and molecular weight. It is also shown that crystal volume scales inversely with molecular weight. The results set the scene for the development of X-ray crystallography in a changing environment for structural biology.

Crystallization and preliminary X-ray analysis of the Escherichia coli UDP-MurNAc-tripeptide D-alanyl-D-alanine-adding enzyme (MurF)

1999 ◽  
Vol 55 (12) ◽  
pp. 2033-2034 ◽  
Author(s):  
Youwei Yan ◽  
Sanjeev Munshi ◽  
Ying Li ◽  
Kelly Ann D. Pryor ◽  
Frank Marsilio ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Data Set ◽  
Solvent Content ◽  
X Ray ◽  
Protein Mass ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystal Volume

Crystals of the Escherichia coli UDP-MurNAc-tripeptide D-Ala-D-Ala-adding protein (MurF), which catalyzes the formation of the last metabolite of the bacterial cell-wall building block, have been grown in hanging-drop vapor-diffusion trials using PEG 8K as a precipitating agent. The crystals belong to hexagonal space group P61 or P65, with unit-cell dimensions a = b = 74, c = 425 Å. The asymmetric unit contains two molecules, with a crystal volume per protein mass (Vm ) of 3.4 Å3 Da−1 and a solvent content of about 64% by volume. A native data set to 2.8 Å resolution has been obtained from a frozen crystal using a synchrotron X-ray source.

Improved crystallographic data for graphite

2003 ◽  
Vol 18 (2) ◽  
pp. 150-154 ◽  
Author(s):  
J. Y. Howe ◽  
C. J. Rawn ◽  
L. E. Jones ◽  
H. Ow
Keyword(s):  
Powder Diffraction ◽  
Figure Of Merit ◽  
Interlayer Spacing ◽  
X Ray Diffraction ◽  
Hexagonal Cell ◽  
Data Set ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Powder diffraction pattern of SP-1 graphite has been obtained using synchrotron X-ray diffraction. Unit cell dimensions were calculated using a least-squares analysis that refined to a |Δ2θ°| of no more than 0.007. A hexagonal cell was determined with a space group of P63/mmc (194), a=2.4617(2) and c=6.7106 (4) Å. The Smith/Synder figure of merit is 167 based upon 11 peaks, which indicates that the quality of this data set is superior to the existing PDF card for graphite, 41-1487. It is also emphasized that the interlayer spacing of graphite should be 3.355(1) Å. Using GAS and EXPGUI codes, a new set of calculated powder diffraction data based upon the interlayer spacing of 3.555 Å is generated. A comparison with the current calculated card, 75-1621, has also been made.

The External Shape of Human γ GI Immunoglobulin from Crystal Sections

1971 ◽  
Vol 29 ◽  
pp. 428-429
Author(s):  
L. W. Labaw
Keyword(s):  
Molecular Weight ◽  
Sodium Phosphate ◽  
Osmium Tetroxide ◽  
Unit Cell ◽  
Monoclinic Space Group ◽  
X Ray ◽  
Large Molecular Weight ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Crystallographic Axes

Crystals of a human γGl immunoglobulin have the external morphology of diamond shaped prisms. X-ray studies have shown them to be monoclinic, space group C2, with 2 molecules per unit cell. The unit cell dimensions are a = 194.1, b = 91.7, c = 51.6Å, 8 = 102°. The relatively large molecular weight of 151,000 and these unit cell dimensions made this a promising crystal to study in the EM.Crystals similar to those used in the x-ray studies were fixed at 5°C for three weeks in a solution of mother liquor containing 5 x 10-5M sodium phosphate, pH 7.0, and 0.03% glutaraldehyde. They were postfixed with 1% osmium tetroxide for 15 min. and embedded in Maraglas the usual way. Sections were cut perpendicular to the three crystallographic axes. Such a section cut with its plane perpendicular to the z direction is shown in Fig. 1.This projection of the crystal in the z direction shows periodicities in at least four different directions but these are only seen clearly by sighting obliquely along the micrograph.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

scholarly journals Crystallization, X-ray diffraction analysis and SIRAS phasing of human α-L-iduronidase

2012 ◽  
Vol 68 (11) ◽  
pp. 1363-1366 ◽  
Author(s):  
Nobuo Maita ◽  
Hisaaki Taniguchi ◽  
Hitoshi Sakuraba
Keyword(s):  
Anomalous Scattering ◽  
Type I ◽  
X Ray Diffraction ◽  
Data Set ◽  
Potassium Tartrate ◽  
Isomorphous Replacement ◽  
Phase Calculation ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Electron Density Map

Human lysosomal α-L-iduronidase, whose deficiency causes mucopolysaccharidosis type I, was crystallized using sodium/potassium tartrate and polyethylene glycol 3350 as a precipitant. Using synchrotron radiation, a native data set was collected from a single crystal at 100 K to 2.3 Å resolution. The crystal belonged to space groupR3 with unit-cell dimensions ofa=b= 259.22,c= 71.83 Å. To obtain the phase information, mercury-derivative crystals were prepared and a single-wavelength anomalous dispersion (SAD) data set was collected at the Hg peak wavelength. Phase calculation with the single isomorphous replacement with anomalous scattering (SIRAS) method successfully yielded an interpretable electron-density map.

Crystallization and preliminary diffraction analysis of the HincII restriction endonuclease–DNA complex

1999 ◽  
Vol 55 (11) ◽  
pp. 1943-1945 ◽  
Author(s):  
Nancy C. Horton ◽  
Lydia F. Dorner ◽  
Ira Schildkraut ◽  
John J. Perona
Keyword(s):  
High Energy ◽  
Asymmetric Unit ◽  
Hanging Drop ◽  
Data Set ◽  
Synchrotron Source ◽  
Polyethylene Glycol 4000 ◽  
Dimeric Complexes ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Dna Complex

Crystals of the 60 kDa dimeric HincII restriction enzyme bound to a 12 base-pair dyad-symmetric duplex DNA carrying the specific 5′-GTCGAC recognition site have been obtained. Crystals grew by hanging-drop vapor diffusion from solutions containing polyethylene glycol 4000 as precipitating agent. The rod-shaped crystals belong to space group I222 (or I212121), with unit-cell dimensions a = 66.9, b = 176.7, c = 256.0 Å. There are most likely to be two dimeric complexes in the asymmetric unit. A complete native data set has been collected from a high-energy synchrotron source to a resolution of 2.5 Å at 100 K, with an R merge of 4.8%.

scholarly journals Structures of pseudo-decagonal approximants in Al−Co−Ni

2012 ◽  
Vol 370 (1969) ◽  
pp. 2949-2959 ◽  
Author(s):  
Sven Hovmöller ◽  
Linus Hovmöller Zou ◽  
Xiaodong Zou ◽  
Benjamin Grushko
Keyword(s):  
High Resolution Electron Microscopy ◽  
Limited Information ◽  
X Ray ◽  
X Ray Crystallography ◽  
Resolution Electron ◽  
Cell Dimensions ◽  
Diffraction Patterns ◽  
Quasi Crystals ◽  
Unit Cell Dimensions ◽  
Microscopy Images

Quasi-crystals shocked the crystallographic world when they were reported in 1984. We now know that they are not a rare exception, and can be found in many alloy systems. One of the richer systems for quasi-crystals and their approximants is Al−Co−Ni. A large series of pseudo-decagonal (PD) approximants have been found. Only two of them, PD4 and PD8, have been solved by X-ray crystallography. We report here the structures of PD1, PD2, PD3 and PD5, solved from the limited information that is provided by electron diffraction patterns, unit cell dimensions and high-resolution electron microscopy images.

Crystallization and preliminary studies of the DNA-binding domain Za from ADAR1 complexed to left-handed DNA

1999 ◽  
Vol 55 (7) ◽  
pp. 1362-1364 ◽  
Author(s):  
Thomas Schwartz ◽  
Karen Shafer ◽  
Ky Lowenhaupt ◽  
Eugene Hanlon ◽  
Alan Herbert ◽  
...  
Keyword(s):  
Raman Spectrum ◽  
Dna Binding ◽  
Diffraction Data ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Data Set ◽  
Left Handed ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

The proteolytically defined Z-DNA binding domain Za of human adenosine deaminase type 1 (hADAR1) has been crystallized in complex with the DNA oligomer d(TCGCGCG). The crystals were obtained from a solution containing ammonium sulfate as precipitating agent and belong to the tetragonal space group P4212. A complete diffraction data set has been collected to a resolution of 2.4 Å. The unit-cell dimensions are a = b = 85.9, c = 71.3 Å. A Raman spectrum of the complex indicates that the DNA in the complex adopts the left-handed Z conformation.

scholarly journals Helicobacter pylori Csd4 is a peptidoglycan metallocarboxypeptidase

2014 ◽  
Vol 70 (a1) ◽  
pp. C442-C442
Author(s):  
Anson Chan ◽  
Yanjie Liu ◽  
Kris Blair ◽  
Emilisa Frirdich ◽  
Erin Gaynor ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Cell Shape ◽  
Diaminopimelic Acid ◽  
Specific Substrate ◽  
Substrate Molecule ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Peptidoglycan Structure ◽  
Unit Cell Dimensions

The bacterial cell wall is a polymeric structure that determines the overall shape of the cell and undergoes constant remodelling during cell growth, requiring enzymes that cleave the existing peptidoglycan structure. Csd4 is an enzyme important for cell shape as deleting it in Helicobacter pylori causes the helical-shaped cells to become rod-like. Csd4 is a zinc carboxypeptidase that can cleave the tripeptide moiety found in peptidoglycan (i.e. L-Ala-γ-D-Glu-m-DAP) to release meso-diaminopimelic acid (mDAP). Structures of Csd4 were solved by X-ray crystallography up to 1.75 Å resolution in space group P212121 with zinc and substrate/product bound and contain the same unit cell dimensions. Csd4 is a monomeric enzyme with three domains: an N-terminal M14-family carboxypeptidase domain followed by two smaller domains likely important in protein-protein or protein-peptidoglycan interactions. Key interactions are observed between the protein and substrate in the active site, supporting specific substrate recognition by Csd4. A water or hydroxide molecule, which is required for catalytic activity, is also observed bound to the zinc and is poised to interact with the substrate molecule upon activation.

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