7H0U
Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0013775-001
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.1 M MES (pH 6.50) and 30 % w/v PEG 4000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.06 | 40.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.86 | α = 90 |
b = 33.12 | β = 96.94 |
c = 60.43 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER2 XE 9M | 2023-09-07 | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04-1 | 0.9212 | Diamond | I04-1 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | |||||
1 | 1.47 | 33.12 | 99.8 | 0.094 | 0.103 | 0.04 | 0.998 | 8.4 | 6.3 | 25573 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.47 | 1.51 | 99.6 | 1.773 | 2.008 | 0.917 | 0.331 | 4.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.47 | 30.25 | 25543 | 1228 | 99.7 | 0.2155 | 0.2138 | 0.2471 | RANDOM | 29.44 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-2.2208 | 2.5579 | 5.9109 | -3.6901 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.14 |
t_omega_torsion | 4.23 |
t_angle_deg | 1.12 |
t_bond_d | 0.011 |
t_dihedral_angle_d | |
t_gen_planes | |
t_it | |
t_chiral_improper_torsion | |
t_ideal_dist_contact |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1263 |
Nucleic Acid Atoms | |
Solvent Atoms | 139 |
Heterogen Atoms | 35 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
Aimless | data scaling |
PHASER | phasing |
XDS | data reduction |