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Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-C-20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.2 M Ammonium phosphate dibasic, 17%
W/v PEG3350, pH8.0
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.642 α = 90 b = 81.338 β = 96.6 c = 90.231 γ = 90
Symmetry Space Group I 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 120 PIXEL Bruker PHOTON II 2022-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54301
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.75 24.29 94.22 0.06357 0.06696 0.02038 0.999 18.88 9 35481 15.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.813 0.3998 0.4645 0.2292 0.935 3.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.75 24.29 1.34 35229 1817 94.26 0.2306 0.2293 0.2295 0.2542 0.2534 25.48
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 7.3391 f_angle_d 1.0708 f_chiral_restr 0.0572 f_plane_restr 0.009 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2367 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms 22
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PROTEUM PLUS data reduction Aimless data scaling PHENIX phasing