7ORV

Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00239


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.7293Protein - 63 mg/mL in 50 mM Tris/HCl pH 8.0, 150 mM NaCl; precipitant (reservoir) - 0.1 M Bis-Tris/HCl pH 6.7, 2.4 M NaCl; 1:1, 1:2, 2:1 protein-to-precipitant ratios, 300 nL total drop volume. Soaking: reservoir solution, supplemented to 50 mM ligand, 5% (v/v) DMSO, 15% (v/v) glycerol; 2 h, 293K.
Crystal Properties
Matthews coefficientSolvent content
3.8768.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.236α = 90
b = 107.236β = 90
c = 107.236γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-11-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX0.9788MAX IVBioMAX

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9528.6699.80.0720.0770.0240.99914.89.915070
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9521001.0151.0680.3330.75210.3

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 REPLACEMENTTHROUGHOUT6ZPE1.9528.661428079099.70.17190.17030.202RANDOM48.683
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.277
r_dihedral_angle_3_deg12.917
r_dihedral_angle_1_deg6.327
r_dihedral_angle_4_deg4.297
r_angle_refined_deg1.335
r_angle_other_deg1.251
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.277
r_dihedral_angle_3_deg12.917
r_dihedral_angle_1_deg6.327
r_dihedral_angle_4_deg4.297
r_angle_refined_deg1.335
r_angle_other_deg1.251
r_chiral_restr0.054
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms909
Nucleic Acid Atoms
Solvent Atoms94
Heterogen Atoms29

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing