7ORU

Non-structural protein 10 (nsp10) from SARS CoV-2 in complex with fragment VT00221


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
3.8267.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.775α = 90
b = 106.775β = 90
c = 106.775γ = 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 BioMAX0.979MAX 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
11.6737.81000.0710.0720.012127.328.623619
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)
11.671.799.71.571.6530.5030.50610.2

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 REPLACEMENTTHROUGHOUT6ZPE1.6737.7822432118499.970.16110.16050.1717RANDOM32.724
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_deg31.681
r_dihedral_angle_3_deg10.195
r_dihedral_angle_1_deg6.155
r_dihedral_angle_4_deg1.878
r_angle_other_deg1.396
r_angle_refined_deg1.379
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.681
r_dihedral_angle_3_deg10.195
r_dihedral_angle_1_deg6.155
r_dihedral_angle_4_deg1.878
r_angle_other_deg1.396
r_angle_refined_deg1.379
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.006
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 Atoms156
Heterogen Atoms29

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing