7L6R

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9292Protein: 3.0 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 2mM SAM, 1mM TCEP, 5% Glycerol; Screen: Ammonium sulfate (E2), 0.1M Citric acid pH 5.0, 0.8M Ammonium sulfate; Soak: 6hours, 0.2mM m7GpppAUUAAA, 5mM SAM, 20mM Manganese chloride in screen solution; Cryo: 25% Sucrose in screen solution.
Crystal Properties
Matthews coefficientSolvent content
4.3371.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.757α = 90
b = 168.757β = 90
c = 52.272γ = 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-D1.54980APS21-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
11.98301000.0950.0950.1010.0320.99731.29.859455-333
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)
11.982.011001.2031.2031.2730.4110.66329.3

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 REPLACEMENTTHROUGHOUT6w4h1.9829.9556344309399.850.15120.15040.1664RANDOM43.986
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]
0.270.130.27-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.775
r_dihedral_angle_4_deg12.724
r_dihedral_angle_3_deg8.359
r_dihedral_angle_1_deg2.922
r_angle_refined_deg1.272
r_angle_other_deg0.372
r_chiral_restr0.057
r_gen_planes_refined0.054
r_gen_planes_other0.048
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.775
r_dihedral_angle_4_deg12.724
r_dihedral_angle_3_deg8.359
r_dihedral_angle_1_deg2.922
r_angle_refined_deg1.272
r_angle_other_deg0.372
r_chiral_restr0.057
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 Atoms3160
Nucleic Acid Atoms118
Solvent Atoms357
Heterogen Atoms96

Software

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