6WKQ

1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in Complex with Sinefungin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6W75PDB entry 6W75

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52925.3 mg/mL 1:1 nsp10/nsp16 in 0.15 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), soak and cryoprotection: 5 mM SFG, 4 M sodium formate, 3 hrs
Crystal Properties
Matthews coefficientSolvent content
3.9568.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 166.247α = 90
b = 166.247β = 90
c = 98.139γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBE2020-04-03MSINGLE 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
11.98301000.0710.0710.0780.03322.25.5108598-331.7
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)
11.982.011000.7840.7840.8740.3840.72425.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 6W751.9829.922108429535799.960.1630.16230.179938.118
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]
0.2830.1410.283-0.917
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.641
r_dihedral_angle_3_deg8.057
r_lrange_it6.904
r_lrange_other6.735
r_dihedral_angle_4_deg5.649
r_scangle_it3.46
r_scangle_other3.46
r_mcangle_it2.656
r_mcangle_other2.655
r_dihedral_angle_1_deg2.463
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg25.641
r_dihedral_angle_3_deg8.057
r_lrange_it6.904
r_lrange_other6.735
r_dihedral_angle_4_deg5.649
r_scangle_it3.46
r_scangle_other3.46
r_mcangle_it2.656
r_mcangle_other2.655
r_dihedral_angle_1_deg2.463
r_scbond_it2.34
r_scbond_other2.327
r_mcbond_it1.603
r_mcbond_other1.603
r_dihedral_angle_other_3_deg1.44
r_angle_refined_deg1.342
r_angle_other_deg0.347
r_nbd_other0.223
r_nbd_refined0.2
r_symmetry_xyhbond_nbd_refined0.177
r_symmetry_nbd_other0.175
r_nbtor_refined0.171
r_symmetry_nbd_refined0.137
r_xyhbond_nbd_refined0.121
r_metal_ion_refined0.121
r_symmetry_nbtor_other0.096
r_chiral_restr0.06
r_gen_planes_refined0.055
r_gen_planes_other0.051
r_symmetry_xyhbond_nbd_other0.01
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6408
Nucleic Acid Atoms
Solvent Atoms636
Heterogen Atoms107

Software

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