6W4H

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52925.3 mg/mL 1:1 nsp16/nsp10 in 0.15 M sodium chloride, 0.01 M Tris, pH 7.5, 2 mM SAM, 1 mM TCEP, 5% glycerol against ComPAS screen A7 (0.2 M calcium acetate, 0.1 M HEPES, pH 7.5, 18% w/v PEG 8000), cryoprotectant: 1:1 screen + 50% sucrose
Crystal Properties
Matthew coefficientSolvent content
4.3371.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.74α = 90
b = 167.74β = 90
c = 51.942γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2020-03-07MSINGLE 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
11.8301000.060.060.0650.02429.37.377886-325.4
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)
11.81.831000.7650.7650.8280.3130.7622.66.8

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 REPLACEMENTTHROUGHOUTPDB entry 3R241.829.7673752382199.970.14970.1490.1627RANDOM31.531
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]
-0.06-0.03-0.060.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.951
r_dihedral_angle_3_deg8.695
r_dihedral_angle_4_deg6.592
r_dihedral_angle_1_deg3.282
r_angle_refined_deg1.183
r_angle_other_deg0.321
r_gen_planes_refined0.055
r_chiral_restr0.052
r_gen_planes_other0.051
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.951
r_dihedral_angle_3_deg8.695
r_dihedral_angle_4_deg6.592
r_dihedral_angle_1_deg3.282
r_angle_refined_deg1.183
r_angle_other_deg0.321
r_gen_planes_refined0.055
r_chiral_restr0.052
r_gen_planes_other0.051
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3201
Nucleic Acid Atoms
Solvent Atoms486
Heterogen Atoms65

Software

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