6WRZ

Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 with 7-methyl-GpppA and S-adenosyl-L-homocysteine in the Active Site and Sulfates in the mRNA Binding Groove.


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: 1mM SAH, 0.5mM GpppA, 2M Lithium sulfate.
Crystal Properties
Matthews coefficientSolvent content
4.371.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.147α = 90
b = 169.147β = 90
c = 51.834γ = 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
12.2530990.0770.0770.0830.0290.99223.47.740141-345.1
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)
12.252.2999.60.8570.8570.9210.3320.792.87.3

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 REPLACEMENTTHROUGHOUT6w4h2.2529.9138166196098.980.16340.1620.1902RANDOM53.482
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]
0.530.260.53-1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.543
r_dihedral_angle_3_deg9.393
r_dihedral_angle_4_deg9.345
r_dihedral_angle_1_deg3.035
r_angle_refined_deg1.246
r_angle_other_deg0.327
r_gen_planes_refined0.054
r_chiral_restr0.052
r_gen_planes_other0.05
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.543
r_dihedral_angle_3_deg9.393
r_dihedral_angle_4_deg9.345
r_dihedral_angle_1_deg3.035
r_angle_refined_deg1.246
r_angle_other_deg0.327
r_gen_planes_refined0.054
r_chiral_restr0.052
r_gen_planes_other0.05
r_bond_refined_d0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3214
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms167

Software

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