6WJT

2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with S-Adenosyl-L-Homocysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W75 

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: ComPAS (F10), 0.4M Potassium/Sodium tartrate; Soak and Cryo: 5mM SAH, 4M Sodium formate, 3 hrs.
Crystal Properties
Matthews coefficientSolvent content
3.9869.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.917α = 90
b = 166.917β = 90
c = 98.099γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe2020-04-03MSINGLE 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)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
12301000.1010.1010.110.04416.76.5105884-334.2
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)
122.031000.7950.7950.8660.340.9333.26.6

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 REPLACEMENTTHROUGHOUT6w75229.79100620523399.80.17210.17110.1911RANDOM40.744
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]
1.350.671.35-4.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.92
r_dihedral_angle_3_deg8.207
r_dihedral_angle_4_deg6.1
r_dihedral_angle_1_deg2.423
r_angle_refined_deg1.33
r_angle_other_deg0.344
r_chiral_restr0.059
r_gen_planes_refined0.055
r_gen_planes_other0.051
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.92
r_dihedral_angle_3_deg8.207
r_dihedral_angle_4_deg6.1
r_dihedral_angle_1_deg2.423
r_angle_refined_deg1.33
r_angle_other_deg0.344
r_chiral_restr0.059
r_gen_planes_refined0.055
r_gen_planes_other0.051
r_bond_refined_d0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6400
Nucleic Acid Atoms
Solvent Atoms596
Heterogen Atoms97

Software

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