6WVN

Crystal Structure of Nsp16-Nsp10 from SARS-CoV-2 in Complex with 7-methyl-GpppA and S-Adenosylmethionine.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W4H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5292Protein: 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: Anions (F3), 0.1M HEPES pH 7.5, 0.9M Sodium phosphate, 0.9M Potassium phosphate; Soak and Cryo: 5mM SAM, 0.5mM GpppA, 2M Lithium sulfate.
Crystal Properties
Matthews coefficientSolvent content
4.3371.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.372α = 90
b = 169.372β = 90
c = 52.083γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE2020-04-17MSINGLE 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
123099.80.070.070.0780.0340.99820.35.158029-337.4
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)
122.031000.8670.8670.9660.4210.7122.055.1

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 REPLACEMENTTHROUGHOUT6w4h229.3554988286699.810.16310.16230.178RANDOM46.88
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]
0.340.170.34-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.392
r_dihedral_angle_4_deg9.617
r_dihedral_angle_3_deg8.564
r_dihedral_angle_1_deg2.684
r_angle_refined_deg1.194
r_angle_other_deg0.31
r_gen_planes_refined0.054
r_chiral_restr0.052
r_gen_planes_other0.051
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.392
r_dihedral_angle_4_deg9.617
r_dihedral_angle_3_deg8.564
r_dihedral_angle_1_deg2.684
r_angle_refined_deg1.194
r_angle_other_deg0.31
r_gen_planes_refined0.054
r_chiral_restr0.052
r_gen_planes_other0.051
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3252
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms50

Software

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