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The crystal structure of SARS-CoV-2 3CLpro with Zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Mes pH 6.5, 15 % PEG20000
Crystal Properties Matthews coefficient Solvent content 1.96 37.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.595 α = 90 b = 53.388 β = 101.429 c = 45.398 γ = 90
Symmetry Space Group C 1 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 PILATUS3 S 6M 2020-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.45 44.5 99 0.078 0.996 10.3 4.1 9708 55.9102488266
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.538 0.614 0.763
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6M2Q 2.45011599532 44.4978033164 1.35000921603 9707 490 99.3551688843 0.199986122321 0.196267853325 0.2022 0.265391631147 0.267 63.7545041307
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 15.3020734835 f_angle_d 1.17995803695 f_chiral_restr 0.0558850197221 f_bond_d 0.00964855371784 f_plane_restr 0.00616851753854
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2317 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing