☰ Navigation Tabs
SARS-CoV-2 Mpro in complex with D-4-38
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y2E 6y2e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 0.2 m ammonium fluoride, 0.2 peg3350, ph=6.2
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.052 α = 90 b = 53.324 β = 100.84 c = 112.859 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 100 PIXEL RIGAKU HyPix-6000HE 2022-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 22.82 99.7 0.998 12.36 4.5 17885
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 99.2 0.721 4.6
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 6y2e 2 22.82 17010 870 99.73 0.189 0.186 0.192 0.2481 0.253 RANDOM 31.171
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] -0.47 0.18 0.44 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.298 r_dihedral_angle_4_deg 16.484 r_dihedral_angle_3_deg 15.141 r_dihedral_angle_1_deg 7.584 r_angle_refined_deg 1.564 r_angle_other_deg 1.327 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.298 r_dihedral_angle_4_deg 16.484 r_dihedral_angle_3_deg 15.141 r_dihedral_angle_1_deg 7.584 r_angle_refined_deg 1.564 r_angle_other_deg 1.327 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2360 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction CrysalisPro data reduction PHASER phasing