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Crystal structure of SARS Cov-2 main protease in complex with an inhibitor 57
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5RGS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.05 M Ammonium sulfate, 0.1 M Sodium Citrate, 15 % (w/v) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.03 39.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.457 α = 90 b = 54.189 β = 99.49 c = 45.701 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 2M 2022-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 1.336 45.08 94.2 0.028 0.019 0.034 0.999 18 3 57524 17.14
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 1.336 1.359 0.465 0.572 0.328 0.804 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 5rgs 1.336 45.08 57471 2869 93.6 0.2021 0.2011 0.1937 0.22 0.2072 RANDOM 20.94
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] -0.3897 1.4179 -0.0663 0.456
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.1 t_omega_torsion 4.45 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.1 t_omega_torsion 4.45 t_angle_deg 1.01 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2279 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 36
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing