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)
TypeSourceAccession CodeDetails
experimental modelPDB 6W4H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6292Protein: 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
Matthews coefficientSolvent content
4.170

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.948α = 90
b = 166.948β = 90
c = 98.81γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE2020-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.05301000.0830.0830.0890.0320.99624.17.699216-335.8
Highest Resolution Shell
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)RedundancyNumber Unique Reflections (All)
12.052.0999.81.0791.0791.1560.4150.7652.17.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6w4h2.0529.9794164502899.880.16670.16580.1846RANDOM47.34
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]
0.630.310.63-2.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.673
r_dihedral_angle_3_deg8.87
r_dihedral_angle_4_deg6.535
r_dihedral_angle_1_deg2.85
r_angle_refined_deg1.29
r_angle_other_deg0.367
r_chiral_restr0.057
r_gen_planes_refined0.054
r_gen_planes_other0.047
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.673
r_dihedral_angle_3_deg8.87
r_dihedral_angle_4_deg6.535
r_dihedral_angle_1_deg2.85
r_angle_refined_deg1.29
r_angle_other_deg0.367
r_chiral_restr0.057
r_gen_planes_refined0.054
r_gen_planes_other0.047
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6490
Nucleic Acid Atoms190
Solvent Atoms545
Heterogen Atoms85

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing