Neutron crystal structure of SARS-CoV-2 NSP3 macrodomain at 293 K (P43 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 | 9.5 | 293 | 100 mM CHES pH 9.5, 34% PEG 3000 |
Crystal Properties |
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Matthews coefficient | Solvent content |
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2.21 | 44.44 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 89.328 | α = 90 |
b = 89.328 | β = 90 |
c = 40.349 | γ = 90 |
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 | 2021-03-29 | M | SINGLE WAVELENGTH |
2 | 1 | neutron | 293 | AREA DETECTOR | ORNL ANGER CAMERA | COLLIMATORS | 2021-03-15 | 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 Spallation Neutron Source BEAMLINE MANDI | 2.00-4.00 | ORNL Spallation Neutron Source | MANDI |
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 | 1.6 | 28.39 | 99.6 | 0.087 | | | 0.038 | 0.996 | | 15.6 | 5.9 | | 42240 | | | |
2 | 1.89 | 14.12 | 94 | 0.217 | | | 0.101 | 0.926 | | 7.2 | 4.4 | | 24142 | | | |
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 | 1.6 | 1.63 | | 0.265 | | | | 0.874 | | 4.6 | 2.8 | |
2 | 1.89 | 1.96 | | 0.2524 | | | | 0.411 | | 2.7 | 3.1 | |
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 | 1.6 | 23.14 | | | | 42212 | 2042 | 99.63 | | | 0.1239 | 0.1576 | RANDOM | 22.64 |
NEUTRON DIFFRACTION | MOLECULAR REPLACEMENT | 1.89 | 14.12 | | | | 24141 | 1173 | 94.01 | | | 0.2258 | 0.275 | RANDOM | 22.64 |
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 | 20.8052 |
f_dihedral_angle_d | 20.8052 |
f_angle_d | 1.474 |
f_angle_d | 1.474 |
f_chiral_restr | 0.0809 |
f_chiral_restr | 0.0809 |
f_bond_d | 0.0119 |
f_bond_d | 0.0119 |
f_plane_restr | 0.0092 |
f_plane_restr | 0.0092 |
Non-Hydrogen Atoms Used in Refinement |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2535 |
Nucleic Acid Atoms | |
Solvent Atoms | 322 |
Heterogen Atoms | 13 |
Software
Software |
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Software Name | Purpose |
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PHENIX | refinement |
Mantid | data reduction |
LAUENORM | data scaling |
PHASER | phasing |
Coot | model building |