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Structure of SARS CoV-2 main protease in complex with Chymostatin.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E91 Only coordinates of protein atoms of molecule A with rem
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 1.8M Ammonium sulfate, 0.1% Bis-Tris ph 6.5, 2%v/v PEG monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2 38.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.184 α = 90 b = 105.231 β = 101.59 c = 54.473 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 Mirror 2021-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 1.12709 SSRL BL11-1
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 1.78 53.36 96.9 0.032 0.999 20.83 3.3 49991 -3 27.52
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 1.78 1.88 97.3 0.53 0.9 2.89 3.27
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 1.78 53.36 47465 2526 97.92 0.20143 0.19915 0.2063 0.2441 0.2531 RANDOM 35.952
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] -1.42 1.5 -0.45 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 6.622 r_long_range_B_refined 6.374 r_long_range_B_other 6.349 r_scangle_other 4.246 r_mcangle_it 3.521 r_mcangle_other 3.52 r_scbond_it 2.745
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.132 r_dihedral_angle_4_deg 14.689 r_dihedral_angle_3_deg 13.203 r_dihedral_angle_1_deg 6.622 r_long_range_B_refined 6.374 r_long_range_B_other 6.349 r_scangle_other 4.246 r_mcangle_it 3.521 r_mcangle_other 3.52 r_scbond_it 2.745 r_scbond_other 2.745 r_mcbond_it 2.34 r_mcbond_other 2.333 r_angle_refined_deg 1.455 r_angle_other_deg 0.829 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4716 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data scaling HKL-3000 data reduction MOLREP phasing