7KOA

Room Temperature Structure of SARS-CoV-2 Nsp10/16 Methyltransferase in a Complex with Cap-0 and SAM Determined by Pink-Beam Serial Crystallography


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE6.5298Protein: 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 polypropylane 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 = 170.86α = 90
b = 170.86β = 90
c = 52.797γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDRAYONIX MX340-HS2020-09-18LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-ID-B1.02-1.18APS14-ID-B

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Nylon Meshfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlSample Solvent
1ALEX mesh holdernylon meshxyz 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
1157181714706

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.449.765.850.12916.57.42279520
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.5115.630.105

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 REPLACEMENTTHROUGHOUT6XKM2.429.5921581119865.790.23620.23390.2766RANDOM39.221
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]
-0.01-0.01-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.064
r_dihedral_angle_3_deg7.728
r_dihedral_angle_4_deg6.979
r_dihedral_angle_1_deg1.931
r_angle_refined_deg1.105
r_angle_other_deg0.264
r_gen_planes_refined0.052
r_gen_planes_other0.046
r_chiral_restr0.043
r_bond_refined_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg21.064
r_dihedral_angle_3_deg7.728
r_dihedral_angle_4_deg6.979
r_dihedral_angle_1_deg1.931
r_angle_refined_deg1.105
r_angle_other_deg0.264
r_gen_planes_refined0.052
r_gen_planes_other0.046
r_chiral_restr0.043
r_bond_refined_d0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3240
Nucleic Acid Atoms
Solvent Atoms182
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
Precognitiondata reduction
Epinormdata scaling