7JPE

Room Temperature Structure of SARS-CoV-2 Nsp10/Nsp16 Methyltransferase in a Complex with m7GpppA Cap-0 and SAM 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 MODE6.5297Protein: 4.0 mg/ml (NSP10/NSP16 1:1), 0.15 M CaCl, 0.01 M Tris-HCl, 2 mM SAM, 1 mM TCEP, 5% Glycerol, pH 7.5. Precipitation buffer: 0.1M MES pH 6.5, 0.9 M NaF. Batch crystallization: 100 ul of protein mixed with 100 ul of precipitation buffer in 500 ul polypropylane tube. Two days before data collection 1 mM EDTA was added to batch crystallization. Crystal were soaked with m7GpppA (0.5 mM) for 10 minutes before data collection.
Crystal Properties
Matthews coefficientSolvent content
4.4972.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.93α = 90
b = 170.93β = 90
c = 52.786γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 X 6MSagittally focusing mono and vertically focusing mirror2020-08-02MSINGLE 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, 1 mM EDTA, 0.5 mM TCEP, 2.5% Glycerol, 0.5 mM m7GpppA
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
15734573474120

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
12.1849.721000.952.5550.514627322.8
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)
12.182.2299.70.3980.5311.42

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 REPLACEMENTTHROUGHOUT6WQ32.1849.7244016221599.870.21790.2170.237RANDOM37.222
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]
-0.23-0.12-0.230.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.054
r_dihedral_angle_3_deg9.069
r_dihedral_angle_4_deg4.736
r_dihedral_angle_1_deg2.273
r_angle_refined_deg1.351
r_angle_other_deg0.37
r_chiral_restr0.059
r_gen_planes_refined0.053
r_gen_planes_other0.049
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.054
r_dihedral_angle_3_deg9.069
r_dihedral_angle_4_deg4.736
r_dihedral_angle_1_deg2.273
r_angle_refined_deg1.351
r_angle_other_deg0.37
r_chiral_restr0.059
r_gen_planes_refined0.053
r_gen_planes_other0.049
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 Atoms131
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
DIALSdata scaling
DIALSdata reduction