Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at 293 K (C2 crystal form)
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) |
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Type | Source | Accession Code | Details |
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experimental model | PDB | 7KQO | |
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 289 | 100 mM MES pH 6.5, 25% PEG 4000 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.53 | 51.35 |
Crystal Data
Unit Cell |
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Length ( ? ) | Angle ( ? ) |
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a = 132.808 | ¦Á = 90 |
b = 36.653 | ¦Â = 98.09 |
c = 38.233 | ¦Ã = 90 |
Symmetry |
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Space Group | C 1 2 1 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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1 | 1 | x-ray | 293 | PIXEL | DECTRIS EIGER R 4M | OSMIC VARIMAX | 2021-08-30 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 293 | AREA DETECTOR | ORNL ANGER CAMERA | COLLIMATORS | 2021-08-30 | L | LAUE |
Radiation Source |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.54 | | |
2 | SPALLATION SOURCE | ORNL High Flux Isotope Reactor BEAMLINE CG4D | 3.3-4.5 | ORNL High Flux Isotope Reactor | CG4D |
Data Collection
Overall |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot |
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1 | 1.95 | 65.74 | 92.9 | 0.07 | | | 0.036 | 0.992 | | 19.2 | 5.6 | | 12576 | | | |
2 | 2.3 | 35.07 | 75.4 | 0.151 | | | 0.118 | 0.954 | | 4.4 | 4 | | 6252 | | | |
Highest Resolution Shell |
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) |
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1 | 1.95 | 2.02 | | 0.236 | | | | 0.954 | | 6 | 5.3 | |
2 | 2.3 | 2.4 | | 0.281 | | | | 0.61 | | 3.2 | 4.4 | |
Refinement
Statistics |
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1.95 | 28.12 | | | | 12572 | 608 | 92.89 | | | 0.1322 | 0.1719 | RANDOM | 33.44 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 2.3 | 32.87 | | | | 6250 | 330 | 75.11 | | | 0.1873 | 0.2592 | RANDOM | 33.44 |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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RMS Deviations |
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Key | Refinement Restraint Deviation |
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f_dihedral_angle_d | 22.5981 |
f_dihedral_angle_d | 22.5981 |
f_angle_d | 1.3541 |
f_angle_d | 1.3541 |
f_chiral_restr | 0.0653 |
f_chiral_restr | 0.0653 |
f_bond_d | 0.0099 |
f_bond_d | 0.0099 |
f_plane_restr | 0.0062 |
f_plane_restr | 0.0062 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 1256 |
Nucleic Acid Atoms | |
Solvent Atoms | 99 |
Heterogen Atoms | 36 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
Coot | model building |
PHASER | phasing |