7JHE

Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with 2'-O-methylated m7GpppA Cap-1 and SAH Determined by Fixed-Target Serial Crystallography


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6WQ3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.5295Protein: 4.0 mg/ml (NSP10/NSP16 1:1), 0.15 M NaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1 M MES pH 6.5, 0.9 M NaF. Batch crystallization: 100 ul of protein mixed with 100 ul of precipitation buffer in 500 ul polypropylene tube. Crystals were soaked with m7GpppA (0.5 mM) for 10 minutes before data collection.
Crystal Properties
Matthews coefficientSolvent content
4.4672.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.859α = 90
b = 170.859β = 90
c = 52.797γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray295PIXELDECTRIS PILATUS3 X 6MSagittally focusing mono and vertically focusing mirror2020-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97918APS19-ID

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Nylon Meshfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1SBC Mesh Holdermeshxyz stageSmarAct Motors viaPMACstart/stop raster over area50 mM MES pH 6.5, 0.45 M NaF, 75 mM NaCl, 5 mM Tris-HCl, 1 mM SAM, 0.5 mM TCEP, 2.5% Glycerol, 0.5 mM m7GpppA
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
177257725105740

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.2549.731000.932.4542.944214521.4
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)
12.252.2999.80.4730.669.28

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 REPLACEMENTTHROUGHOUT6WQ32.2549.7340062206599.930.22430.22310.2485RANDOM37.147
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.016
r_dihedral_angle_3_deg10.373
r_dihedral_angle_4_deg9.598
r_dihedral_angle_1_deg3.003
r_angle_refined_deg1.353
r_angle_other_deg0.356
r_gen_planes_refined0.053
r_chiral_restr0.052
r_gen_planes_other0.05
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.016
r_dihedral_angle_3_deg10.373
r_dihedral_angle_4_deg9.598
r_dihedral_angle_1_deg3.003
r_angle_refined_deg1.353
r_angle_other_deg0.356
r_gen_planes_refined0.053
r_chiral_restr0.052
r_gen_planes_other0.05
r_bond_refined_d0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3193
Nucleic Acid Atoms
Solvent Atoms160
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
DIALSdata scaling
DIALSdata reduction