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Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the WZ16 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 8% w/v PEG 8,000;
0.2 M NaCl;
0.1 M MES pH 6
Crystal Properties Matthews coefficient Solvent content 4.55 72.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.011 α = 90 b = 168.011 β = 90 c = 52.085 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 200K 2021-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541870
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 35.49 100 0.603 0.6365 0.968 4.64 9.9 29361 38.1375147861
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 100 3.751 3.95 0.235 0.7 10.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6YZ1 2.5 35.49 1.34349584923 29347 1468 99.8842789558 0.233049431931 0.232024244221 0.2333 0.252118171954 0.2521 random selection 42.5248784989
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 Key Refinement Restraint Deviation f_dihedral_angle_d 16.0350965775 f_angle_d 0.970425368248 f_chiral_restr 0.0363659616366 f_bond_d 0.0317792661117 f_plane_restr 0.00257559331884
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3126 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 92
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing Coot model building PHENIX refinement