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Crystal structure of SARS CoV-2 3CLpro (Mpro) with ALG-097078
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Proprietary model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.25 293 PEG 2000 MME, Bis-Tris
Crystal Properties Matthews coefficient Solvent content 2.25 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.283 α = 90 b = 99.039 β = 108.19 c = 59.08 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2020-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000040 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 1.282 56.128 94 0.037 0.037 0.02 0.999 15.9 4 145163
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.282 1.304 60.3 0.689 0.689 0.504 0.609 1.3 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.282 56.128 137965 7192 94.01 0.1736 0.1728 0.182 0.1896 0.1974 RANDOM 22.239
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] -0.11 -0.61 -0.02 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_4_deg 11.801 r_dihedral_angle_1_deg 6.741 r_mcangle_it 3.361 r_mcbond_it 2.45 r_mcbond_other 2.435 r_angle_refined_deg 1.704 r_angle_other_deg 1.366 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.979 r_dihedral_angle_3_deg 13.588 r_dihedral_angle_4_deg 11.801 r_dihedral_angle_1_deg 6.741 r_mcangle_it 3.361 r_mcbond_it 2.45 r_mcbond_other 2.435 r_angle_refined_deg 1.704 r_angle_other_deg 1.366 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4698 Nucleic Acid Atoms Solvent Atoms 638 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction autoPROC data reduction XDS data reduction Aimless data scaling PHASER phasing