7JIB

Room Temperature Crystal Structure of Nsp10/Nsp16 from SARS-CoV-2 with Substrates and Products of 2'-O-methylation of the Cap-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6WQ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295Protein: 4.0 mg/ml (Nsp10/Nsp16 1:1), 0.15 M NaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1 M MES pH 6.5, 0.9 M NaF. Sitting drops made using 0.4 ul of protein mixed with 0.4 ul of precipitation buffer.
Crystal Properties
Matthews coefficientSolvent content
4.4972.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.83α = 90
b = 170.83β = 90
c = 52.738γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELDECTRIS PILATUS3 X 6M2020-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.655099.60.1480.0710.981155.225799-349.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.799.81.0370.5070.5371.874.9

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 REPLACEMENTTHROUGHOUT6WQ32.6529.5924366126098.960.15620.15490.1809RANDOM55.906
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]
-0.31-0.15-0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.658
r_dihedral_angle_3_deg8.603
r_dihedral_angle_4_deg8.08
r_dihedral_angle_1_deg2.042
r_angle_refined_deg1.291
r_angle_other_deg0.326
r_gen_planes_refined0.053
r_chiral_restr0.052
r_gen_planes_other0.05
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.658
r_dihedral_angle_3_deg8.603
r_dihedral_angle_4_deg8.08
r_dihedral_angle_1_deg2.042
r_angle_refined_deg1.291
r_angle_other_deg0.326
r_gen_planes_refined0.053
r_chiral_restr0.052
r_gen_planes_other0.05
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3184
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms193

Software

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