7L6T

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.


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: 6hours, 0.2mM m7GpppAUUAAA, 5mM SAM, in screen solution;Cryo: 25% Sucrose in screen solution.
Crystal Properties
Matthews coefficientSolvent content
4.3972

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.351α = 90
b = 169.351β = 90
c = 52.629γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MBe2020-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.12708APS21-ID-D

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
11.783096.60.090.090.0970.0360.99620.86.881048-324.4
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)
11.781.8184.21.1561.1561.2690.5130.562.15.8

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 REPLACEMENTTHROUGHOUT6w4h1.7829.3376229395096.810.14180.14080.1615RANDOM33.036
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]
0.750.380.75-2.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.239
r_dihedral_angle_3_deg8.898
r_dihedral_angle_4_deg7.69
r_dihedral_angle_1_deg3.421
r_angle_refined_deg1.33
r_angle_other_deg0.379
r_chiral_restr0.064
r_gen_planes_refined0.054
r_gen_planes_other0.048
r_bond_refined_d0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.239
r_dihedral_angle_3_deg8.898
r_dihedral_angle_4_deg7.69
r_dihedral_angle_1_deg3.421
r_angle_refined_deg1.33
r_angle_other_deg0.379
r_chiral_restr0.064
r_gen_planes_refined0.054
r_gen_planes_other0.048
r_bond_refined_d0.006
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3191
Nucleic Acid Atoms96
Solvent Atoms531
Heterogen Atoms70

Software

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