9EUN

SARS-CoV-2 nsp10-16 methyltransferase in complex with SAM and m7GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7JIB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293.15400 mM sodium fluoride, 100 mM 2-(N-morpholino)ethanesulfonic acid
Crystal Properties
Matthews coefficientSolvent content
4.371.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.55α = 90
b = 167.55β = 90
c = 52.05γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.033220PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.3348.9999.890.40430.42230.12130.9894.62126985748.47
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.332.3999.933.3383.51.0460.2020.3511

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.3348.991.3536004180199.890.18950.18710.234452.09
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.708
f_angle_d1.2005
f_chiral_restr0.059
f_bond_d0.0114
f_plane_restr0.0092
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3212
Nucleic Acid Atoms
Solvent Atoms186
Heterogen Atoms118

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
Cootmodel building
PHENIXphasing