9P6P | pdb_00009p6p

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5292Protein: 3.8 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Classics II (B3), 0.5M Magnesium formate, 0.1M HEPES pH 7.5; Soak: 0.5 hours, 0.2mM m7GpppAUU, 5mM SAH, in 2M Lithium sulfate.
Crystal Properties
Matthews coefficientSolvent content
4.1470.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.471α = 90
b = 168.471β = 90
c = 99.945γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97913APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.95301000.1670.1670.0640.99215.37.9117967-334
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.981000.431.67.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.9529.46112081586199.840.16930.1680.17410.19250.1978RANDOM45.607
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]
0.480.240.48-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.237
r_dihedral_angle_4_deg10.765
r_dihedral_angle_3_deg9.645
r_dihedral_angle_1_deg3.278
r_angle_refined_deg1.223
r_angle_other_deg0.32
r_chiral_restr0.059
r_gen_planes_refined0.054
r_gen_planes_other0.048
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.237
r_dihedral_angle_4_deg10.765
r_dihedral_angle_3_deg9.645
r_dihedral_angle_1_deg3.278
r_angle_refined_deg1.223
r_angle_other_deg0.32
r_chiral_restr0.059
r_gen_planes_refined0.054
r_gen_planes_other0.048
r_bond_refined_d0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6482
Nucleic Acid Atoms182
Solvent Atoms538
Heterogen Atoms195

Software

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