7JYY
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6W4H |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 5.6 | 292 | Protein: 5.3 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: ComPAS (G5), 0.1M Sodium citrate pH 5.6, 1.0M Ammonium dihydrogen phosphate; Soak: 1.5 hours, 0.2mM [M7Gppp]rArUrUrArArA, 5mM SAM, 5mM Manganese chloride; Cryo: 4M Sodium formate. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.1 | 70 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 166.948 | α = 90 |
b = 166.948 | β = 90 |
c = 98.81 | 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 | 2020-07-31 | 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) | 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 | 2.05 | 30 | 100 | 0.083 | 0.083 | 0.089 | 0.032 | 0.996 | 24.1 | 7.6 | 99216 | -3 | 35.8 |
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 | 2.05 | 2.09 | 99.8 | 1.079 | 1.079 | 1.156 | 0.415 | 0.765 | 2.1 | 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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6w4h | 2.05 | 29.97 | 94164 | 5028 | 99.88 | 0.1667 | 0.1658 | 0.1846 | RANDOM | 47.34 |
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] | |
0.63 | 0.31 | 0.63 | -2.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 27.673 |
r_dihedral_angle_3_deg | 8.87 |
r_dihedral_angle_4_deg | 6.535 |
r_dihedral_angle_1_deg | 2.85 |
r_angle_refined_deg | 1.29 |
r_angle_other_deg | 0.367 |
r_chiral_restr | 0.057 |
r_gen_planes_refined | 0.054 |
r_gen_planes_other | 0.047 |
r_bond_refined_d | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6490 |
Nucleic Acid Atoms | 190 |
Solvent Atoms | 545 |
Heterogen Atoms | 85 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHASER | phasing |