6XKM

Room Temperature Structure of SARS-CoV-2 NSP10/NSP16 Methyltransferase in a Complex with SAM Determined by Fixed-Target Serial Crystallography


X-RAY DIFFRACTION

Starting Model(s)

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

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.
Crystal Properties
Matthews coefficientSolvent content
4.4972.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.41α = 90
b = 170.41β = 90
c = 52.631γ = 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 via PMACstart/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
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
1109901099073100

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
12.2549.571000.9682.6882.414177023.2
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)
12.252.2999.70.4490.5810.24

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 REPLACEMENTTHROUGHOUT6W4H2.2549.5739686205499.890.20680.20650.2126RANDOM37.635
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]
-0.29-0.15-0.290.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.727
r_dihedral_angle_3_deg9.938
r_dihedral_angle_4_deg7.562
r_dihedral_angle_1_deg2.98
r_angle_refined_deg1.217
r_angle_other_deg0.323
r_gen_planes_refined0.053
r_chiral_restr0.049
r_gen_planes_other0.049
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.727
r_dihedral_angle_3_deg9.938
r_dihedral_angle_4_deg7.562
r_dihedral_angle_1_deg2.98
r_angle_refined_deg1.217
r_angle_other_deg0.323
r_gen_planes_refined0.053
r_chiral_restr0.049
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 Atoms3188
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing
DIALSdata scaling
DIALSdata reduction