High-resolution macromolecular crystallography at the FemtoMAX beamline with time-over-threshold photon detection

Protein dynamics contribute to protein function on different time scales. Ultrafast X-ray diffraction snapshots can visualize the location and amplitude of atom displacements after perturbation. Since amplitudes of ultrafast motions are small, high-quality X-ray diffraction data is necessary for detection. Diffraction from bovine trypsin crystals using single femtosecond X-ray pulses was recorded at FemtoMAX, which is a versatile beamline of the MAX IV synchrotron. The time-over-threshold detection made it possible that single photons are distinguishable even under short-pulse low-repetition-rate conditions. The diffraction data quality from FemtoMAX beamline enables atomic resolution investigation of protein structures. This evaluation is based on the shape of the Wilson plot, cumulative intensity distribution compared with theoretical distribution, I/σ, R merge/R meas and CC1/2 statistics versus resolution. The FemtoMAX beamline provides an interesting alternative to X-ray free-electron lasers when studying reversible processes in protein crystals.

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HiSPoD: a program for high-speed polychromatic X-ray diffraction experiments and data analysis on polycrystalline samples

Journal of Synchrotron Radiation ◽

10.1107/s1600577516005804 ◽

2016 ◽

Vol 23 (4) ◽

pp. 1046-1053 ◽

Cited By ~ 21

Author(s):

Tao Sun ◽

Kamel Fezzaa

Keyword(s):

Diffraction Data ◽

High Speed ◽

Short Pulse ◽

Frame Rate ◽

Short Exposure ◽

X Rays ◽

X Ray Diffraction ◽

Short Exposure Time ◽

X Ray ◽

Structure Information

A high-speed X-ray diffraction technique was recently developed at the 32-ID-B beamline of the Advanced Photon Source for studying highly dynamic, yet non-repeatable and irreversible, materials processes. In experiments, the microstructure evolution in a single material event is probed by recording a series of diffraction patterns with extremely short exposure time and high frame rate. Owing to the limited flux in a short pulse and the polychromatic nature of the incident X-rays, analysis of the diffraction data is challenging. Here,HiSPoD, a stand-alone Matlab-based software for analyzing the polychromatic X-ray diffraction data from polycrystalline samples, is described. WithHiSPoD, researchers are able to perform diffraction peak indexing, extraction of one-dimensional intensity profiles by integrating a two-dimensional diffraction pattern, and, more importantly, quantitative numerical simulations to obtain precise sample structure information.

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A Robust Method for Collecting X-ray Diffraction Data from Protein Crystals across Physiological Temperatures

10.1101/2020.03.17.995852 ◽

2020 ◽

Cited By ~ 3

Author(s):

Tzanko Doukov ◽

Daniel Herschlag ◽

Filip Yabukarski

Keyword(s):

Diffraction Data ◽

Protein Function ◽

Three Dimensional ◽

Proteinase K ◽

Protein Crystals ◽

X Ray Diffraction ◽

X Ray ◽

Conformational Ensembles ◽

X Ray Crystallography ◽

Lysozyme Crystals

AbstractTraditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure-function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Further, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that is directly related to biological function. The next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperatures and was addressed herein. This approach provides complete diffraction datasets with total collection times as short as ~5 sec from single protein crystals, dramatically increasing the amount of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09-1.54 Å resolution data over a temperature range of 293–363 K for proteinase K, thaumatin, and lysozyme crystals. Our analyses indicate that the diffraction data is of high-quality and do not suffer from excessive dehydration or damage.

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Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures

Journal of Applied Crystallography ◽

10.1107/s1600576720013503 ◽

2020 ◽

Vol 53 (6) ◽

pp. 1493-1501

Author(s):

Tzanko Doukov ◽

Daniel Herschlag ◽

Filip Yabukarski

Keyword(s):

Radiation Damage ◽

Diffraction Data ◽

Protein Function ◽

Room Temperature ◽

Three Dimensional ◽

Proteinase K ◽

Protein Crystals ◽

X Ray Diffraction ◽

X Ray ◽

Conformational Ensembles

Traditional X-ray diffraction data collected at cryo-temperatures have delivered invaluable insights into the three-dimensional structures of proteins, providing the backbone of structure–function studies. While cryo-cooling mitigates radiation damage, cryo-temperatures can alter protein conformational ensembles and solvent structure. Furthermore, conformational ensembles underlie protein function and energetics, and recent advances in room-temperature X-ray crystallography have delivered conformational heterogeneity information that can be directly related to biological function. Given this capability, the next challenge is to develop a robust and broadly applicable method to collect single-crystal X-ray diffraction data at and above room temperature. This challenge is addressed herein. The approach described provides complete diffraction data sets with total collection times as short as ∼5 s from single protein crystals, dramatically increasing the quantity of data that can be collected within allocated synchrotron beam time. Its applicability was demonstrated by collecting 1.09–1.54 Å resolution data over a temperature range of 293–363 K for proteinase K, thaumatin and lysozyme crystals at BL14-1 at the Stanford Synchrotron Radiation Lightsource. The analyses presented here indicate that the diffraction data are of high quality and do not suffer from excessive dehydration or radiation damage.

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High-pressure synthesis and crystal structure of the mixed-cation borate Ga4In4B15O33(OH)3

Zeitschrift für Naturforschung B ◽

10.1515/znb-2019-0014 ◽

2019 ◽

Vol 74 (4) ◽

pp. 357-363

Author(s):

Daniela Vitzthum ◽

Hubert Huppertz

Keyword(s):

Crystal Structure ◽

High Pressure ◽

High Temperature ◽

Diffraction Data ◽

X Ray Diffraction ◽

Synthesis And Crystal Structure ◽

X Ray ◽

Mixed Cation ◽

High Pressure High Temperature ◽

Pressure Synthesis

AbstractThe mixed cation triel borate Ga4In4B15O33(OH)3 was synthesized in a Walker-type multianvil apparatus at high-pressure/high-temperature conditions of 12.5 GPa and 1300°C. Although the product could not be reproduced in further experiments, its crystal structure could be reliably determined via single-crystal X-ray diffraction data. Ga4In4B15O33(OH)3 crystallizes in the tetragonal space group I41/a (origin choice 2) with the lattice parameters a = 11.382(2), c = 15.244(2) Å, and V = 1974.9(4) Å3. The structure of the quaternary triel borate consists of a complex network of BO4 tetrahedra, edge-sharing InO6 octahedra in dinuclear units, and very dense edge-sharing GaO6 octahedra in tetranuclear units.

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Crystallization and preliminary x-ray diffraction data of the cryptomonad biliprotein phycocyanin-645 from a Chroomonas spec.

Archives of Microbiology ◽

10.1007/bf00454927 ◽

1984 ◽

Vol 140 (2-3) ◽

pp. 202-205 ◽

Cited By ~ 14

Author(s):

Walter Morisset ◽

Werner Wehrmeyer ◽

Tilman Schirmer ◽

Wolfram Bode

Keyword(s):

Diffraction Data ◽

X Ray Diffraction ◽

X Ray

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Theoretically derived thermodynamic properties can be improved by the refinement of low-frequency modes against X-ray diffraction data

Chemical Communications ◽

10.1039/d1cc02608a ◽

2021 ◽

Author(s):

Anna Agnieszka Hoser ◽

Marcin Sztylko ◽

Damian Trzybiński ◽

Anders Østergaard Madsen

Keyword(s):

Thermodynamic Properties ◽

Dft Calculations ◽

Diffraction Data ◽

Molecular Crystals ◽

Low Frequency ◽

X Ray Diffraction ◽

X Ray ◽

Efficient Approach

A framework for estimation of thermodynamic properties for molecular crystals via refinement of frequencies from DFT calculations against X-ray diffraction data is presented. The framework provides an efficient approach to...

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Transient phase fraction and dislocation density estimation from in-situ X-ray diffraction data with a low signal-to-noise ratio using a Bayesian approach to the Rietveld analysis

Materials Characterization ◽

10.1016/j.matchar.2020.110860 ◽

2020 ◽

pp. 110860

Author(s):

Manfred Wiessner ◽

Paul Angerer ◽

Sybrand van der Zwaag ◽

Ernst Gamsjäger

Keyword(s):

Dislocation Density ◽

Density Estimation ◽

Diffraction Data ◽

Signal To Noise Ratio ◽

Rietveld Analysis ◽

Transient Phase ◽

X Ray Diffraction ◽

Signal To Noise ◽

X Ray

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Single-crystal investigation of Ce5AgxGe4−x (x = 0.1−1.08) with Sm5Ge4 type

Zeitschrift für Naturforschung B ◽

10.1515/znb-2020-0091 ◽

2020 ◽

Vol 75 (8) ◽

pp. 765-768

Author(s):

Bohdana Belan ◽

Dorota Kowalska ◽

Mariya Dzevenko ◽

Mykola Manyako ◽

Roman Gladyshevskii

Keyword(s):

Crystal Structure ◽

Single Crystal ◽

Diffraction Data ◽

Binary Compound ◽

Lattice Parameters ◽

X Ray Diffraction ◽

Space Group ◽

X Ray

AbstractThe crystal structure of the phase Ce5AgxGe4−x (x = 0.1−1.08) has been determined using single-crystal X-ray diffraction data for Ce5Ag0.1Ge3.9. This phase is isotypic with Sm5Ge4: space group Pnma (No. 62), Pearson code oP36, Z = 4, a = 7.9632(2), b = 15.2693(5), c = 8.0803(2) Å; R1 = 0.0261, wR2 = 0.0460, 1428 F2 values and 48 variables. The two crystallographic positions 8d and 4c show Ge/Ag mixing, leading to a slight increase in the lattice parameters as compared to those of the pure binary compound Ce5Ge4.

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Optimization in S-SAD phasing - difference between solved and unsolved structure

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314093863 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C613-C613

Author(s):

Jan Stránský ◽

Tomáš Kovaľ ◽

Lars Østergaard ◽

Jarmila Dušková ◽

Tereza Skálová ◽

...

Keyword(s):

Data Processing ◽

De Novo ◽

Protein Structures ◽

X Ray Diffraction ◽

X Ray ◽

Structure Solution ◽

Sad Phasing ◽

Optimal Values ◽

Grant Agency ◽

Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

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