6W75
1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex from SARS-CoV-2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6W4H | PDB entry 6W4H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8.3 | 292 | 9.7 mg/mL 1:1 nsp10/nsp16 in 0.5 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), cryoprotectant: 4 M sodium formate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.87 | 68.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 166.245 | α = 90 |
b = 166.245 | β = 90 |
c = 98.279 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARMOSAIC 300 mm CCD | Be | 2020-03-07 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
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) | 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 | 1.95 | 30 | 100 | 0.077 | 0.077 | 0.083 | 0.03 | 25.8 | 7.6 | 113483 | -3 | 28.4 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
1 | 1.95 | 1.98 | 100 | 0.742 | 0.742 | 0.795 | 0.285 | 0.88 | 3.2 | 7.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 6W4H | 1.951 | 29.925 | 113455 | 5610 | 99.893 | 0.158 | 0.1573 | 0.1745 | 33.856 |
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] | |
0.578 | 0.289 | 0.578 | -1.876 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.895 |
r_dihedral_angle_3_deg | 8.996 |
r_dihedral_angle_4_deg | 7.019 |
r_lrange_it | 6.614 |
r_lrange_other | 6.425 |
r_dihedral_angle_1_deg | 3.157 |
r_scangle_it | 2.853 |
r_scangle_other | 2.853 |
r_mcangle_it | 2.194 |
r_mcangle_other | 2.194 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6384 |
Nucleic Acid Atoms | |
Solvent Atoms | 745 |
Heterogen Atoms | 125 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |