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.

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.

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.

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 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.

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.

Electron Microscopy of Alcohol Oxidase Crystals from Pichia Pastoris

1990 ◽  
Vol 48 (1) ◽  
pp. 108-109
Author(s):  
Janet Vonck ◽  
Ernst F.J. van Bruggen
Keyword(s):  
Pichia Pastoris ◽  
Hansenula Polymorpha ◽  
Alcohol Oxidase ◽  
Unit Cell ◽  
Electron Microscopic ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cell Dimensions ◽  
Microscopic Studies ◽  
Unit Cell Dimensions

Several yeast species are able to grow on methanol. When they are grown in a methanol-restricted culture, their peroxisomes contain large crystalline inclusions, consisting of alcohol oxidase (AOX). A monomer of AOX has a molecular weight of ca. 74,000. Inside the peroxisome, AOX occurs as octamers.Electron microscopic studies of AOX from Hansenula polymorpha have revealed that the eight subunits are slightly elongated and form two layers of four, which are twisted relative to each other. The molecule measures ca. 12 nm in all directions.Recently, crystals suitable for x-ray diffraction have been formed of AOX from Pichia pastoris . The space group is P21, with unit cell dimensions a=157.3Å, b=171.45Å, c=231.6Å, β=94°. These dimensions indicate that the unit cell contains four octamers, too much to solve by x-ray crystallography alone. Therefore, we have started an EM study of the crystals, to get information about the organization of the molecules in the crystal lattice.

Structure and Conformation of Photosynthetic Pigments and Related Compounds, 8 [1]Molecular Structure of an Iron(III) Chlorophyll Derivative-Chloro(phytochlorinato methyl ester)iron(III)

1995 ◽  
Vol 50 (1) ◽  
pp. 139-146 ◽  
Author(s):  
Mathias O. Senge ◽  
Karin Ruhlandt-Senge ◽  
Kevin M. Smith
Keyword(s):  
Molecular Structure ◽  
Crystal And Molecular Structure ◽  
Axial Ligand ◽  
Monoclinic Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Chlorophyll Derivative ◽  
Cell Dimensions ◽  
Unit Cell Dimensions ◽  
Related Compounds

The crystal and molecular structure of chloro(methyl phytochlorinato)iron(III), 4, have been determined by single crystal X-ray crystallography to obtain further information on the conformation of metallochlorins related to chlorophyll. The compound crystallized with two independent molecules mainly distinguished by the orientation of the axial ligand. The macrocycles show significant deviations from planarity larger than those observed in corresponding magnesium(II) complexes. The overall type of distortion is similar to those found in chlorophyllides. Compound 4 crystallized in the monoclinic space group P21 (MoKa,λ = 0.71063 A) with unit cell dimensions a = 12.035(6) Å, b = 13.396(8) Å, c = 19.04(2), b = 97.51(2) Å, Z = 4, V = 3043(4) Å3. The structure was refined to an R-value of 0.075 on the basis of 3974 reflections with I > 3.0σ(Ι) (130 Κ).

Strukturen sterisch überfüllter Moleküle, 39 [1,2]

1994 ◽  
Vol 49 (2) ◽  
pp. 288-296 ◽  
Author(s):  
H. Bock ◽  
J. Meuret ◽  
J. W. Bats ◽  
Z. Havlas
Keyword(s):  
Gas Phase ◽  
Phase Structure ◽  
Measured Data ◽  
Dihedral Angles ◽  
Vacuum Sublimation ◽  
Cell Dimensions ◽  
Gas Phase Structure ◽  
Unit Cell Dimensions ◽  
Monosubstituted Derivative

1,4-Bis(trimethylsiloxy)benzene has been crystallized both by vacuum sublimation and from «-heptane solution, which each yielded colourless plates with identical monoclinic unit cell dimensions (P2/n, Z = 4). The conformation of C[ symmetry shows the two (H3C)3SiO-substituents to be conrotationally twisted around the O-( C6H4)-O axis by dihedral angles o f ± 60°. According to the photoelectron spectroscopic ionisation pattern and its Koopmans’ assignment, IEVn = -εJAM 1, by AM 1 eigenvalues, the gas phase structure should also be of C, symmetry. The results of geometry-optimized MNDO , AM 1 or PM 3 calculations for the monosubstituted derivative H5C6-OS i(CH3)3 are compared with respect to the quality of their fit to the measured data.

scholarly journals Crystal and Molecular Structure of Platinum(II) Complex with Bis(Diphenyl Phosphino)Methane

2019 ◽  
Vol 35 (5) ◽  
pp. 1546-1549
Author(s):  
Karwan Omer Ali ◽  
Hikmat Ali Mohammad ◽  
Thomas Gerber ◽  
Eric Hosten
Keyword(s):  
Crystal And Molecular Structure ◽  
Complex Structure ◽  
Complex Form ◽  
Monoclinic Crystal ◽  
Calculated Density ◽  
X Ray ◽  
X Ray Crystallography ◽  
Square Planar ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Platinum(II) complex consisting of the tertiarydiphosphine (dppm) ligand had been prepared from PdCl2 with one equiv. of dppm ligand to form [PtC2(dppmCl)] complex where as dppmCl is bis(dipheny1phosphino) chloromethene. Crystal was grown in dichloromethane by slow evaporation process and characterized by X-ray crystallography technic. The complex structure synthesized based upon the identification using X-ray Crystallography and FTIR was [PtC12(dppmCl)], the ligand dppm coordinated to the meta centre as bidentate chelating ligand and form square planar arrangement around Pt(II) metal centre. The bond distances of Pt-P1, Pt-P2, Pt- Cl1 and Pt-Cl2 are 2.217 (2), 2.217 (2), 2.3661 (19) and 2.3661 Aο respectively. The characterized results of Pt(II) complex using X-ray analysis illustrated that [PtC12(dppmCl)] Complex form monoclinic crystal with unit cell dimensions of a = 16.2034(5), b = 7.8274(2), and c = 19.2496 (6) Aο, with β = 98.918 (1)ο, Z=4, calculated density= 1.838 mg/m3, T= 200 k and space group C2/c

Preliminary X-ray analysis of a new crystal form of recombinant pig kidney DOPA decarboxylase

1999 ◽  
Vol 55 (2) ◽  
pp. 568-570 ◽  
Author(s):  
V. N. Malashkevich ◽  
P. Burkhard ◽  
P. Dominici ◽  
P. S. Moore ◽  
C. Borri Voltattorni ◽  
...  
Keyword(s):  
Heavy Atom ◽  
Crystal Form ◽  
Dopa Decarboxylase ◽  
Data Sets ◽  
Synchrotron Source ◽  
Pig Kidney ◽  
Protein Dimers ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

DOPA decarboxylase is responsible for the synthesis of the key neurotransmitters dopamine and serotonin via decarboxylation of L-3,4-dihydroxyphenylalanine (L-DOPA) and L-5-hydroxytryptophan, respectively. The crystals of recombinant DOPA decarboxylase differ from those previously reported for the enzyme purified from pig kidney. They belong to space group P622 with unit-cell dimensions a = b = 302.6, c = 178.1 Å. Both the self-rotation function and the good diffraction quality of these crystals (2.5 Å on a synchrotron source) suggest that there should be at least three protein dimers in the asymmetric unit. Diffraction data sets have been collected for the native enzyme and a heavy-atom derivative.

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