6W75

1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex from SARS-CoV-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W4HPDB entry 6W4H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.32929.7 mg/mL 1:1 nsp10/nsp16 in 0.5 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen F10 (0.4 M potassium/sodium tartrate), cryoprotectant: 4 M sodium formate
Crystal Properties
Matthews coefficientSolvent content
3.8768.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.245α = 90
b = 166.245β = 90
c = 98.279γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe2020-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.95301000.0770.0770.0830.0325.87.6113483-328.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.981000.7420.7420.7950.2850.883.27.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 6W4H1.95129.925113455561099.8930.1580.15730.174533.856
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]
0.5780.2890.578-1.876
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.895
r_dihedral_angle_3_deg8.996
r_dihedral_angle_4_deg7.019
r_lrange_it6.614
r_lrange_other6.425
r_dihedral_angle_1_deg3.157
r_scangle_it2.853
r_scangle_other2.853
r_mcangle_it2.194
r_mcangle_other2.194
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.895
r_dihedral_angle_3_deg8.996
r_dihedral_angle_4_deg7.019
r_lrange_it6.614
r_lrange_other6.425
r_dihedral_angle_1_deg3.157
r_scangle_it2.853
r_scangle_other2.853
r_mcangle_it2.194
r_mcangle_other2.194
r_scbond_it1.971
r_scbond_other1.914
r_mcbond_it1.31
r_mcbond_other1.31
r_angle_refined_deg1.286
r_angle_other_deg0.329
r_nbd_other0.234
r_nbd_refined0.203
r_symmetry_nbd_other0.17
r_nbtor_refined0.17
r_symmetry_nbd_refined0.149
r_metal_ion_refined0.147
r_xyhbond_nbd_refined0.142
r_symmetry_xyhbond_nbd_refined0.135
r_symmetry_xyhbond_nbd_other0.118
r_symmetry_nbtor_other0.095
r_chiral_restr0.058
r_gen_planes_refined0.055
r_gen_planes_other0.051
r_bond_refined_d0.005
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6384
Nucleic Acid Atoms
Solvent Atoms745
Heterogen Atoms125

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing