6WKS

Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3R24 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION729310% (v/v) MPD, 0.1M HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
4.4472.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.067α = 90
b = 168.067β = 90
c = 52.304γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2020-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

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
11.830.00299.90.130.130.130.0420.99713.620.027840134.91
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)
11.81.8671001.6561.6581.6980.37420.7071.3518.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3r241.830.00278401390999.9720.1540.1520.18843.686
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]
-0.342-0.171-0.3421.111
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.896
r_dihedral_angle_4_deg17.672
r_dihedral_angle_3_deg14.392
r_scangle_it9.964
r_scbond_it8.785
r_lrange_it8.725
r_mcangle_it7.228
r_rigid_bond_restr6.541
r_dihedral_angle_1_deg6.316
r_mcbond_it6.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.896
r_dihedral_angle_4_deg17.672
r_dihedral_angle_3_deg14.392
r_scangle_it9.964
r_scbond_it8.785
r_lrange_it8.725
r_mcangle_it7.228
r_rigid_bond_restr6.541
r_dihedral_angle_1_deg6.316
r_mcbond_it6.118
r_angle_refined_deg1.851
r_nbtor_refined0.313
r_symmetry_nbd_refined0.233
r_nbd_refined0.21
r_xyhbond_nbd_refined0.158
r_symmetry_xyhbond_nbd_refined0.126
r_chiral_restr0.124
r_bond_refined_d0.015
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3163
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms103

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing