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Complex structure of HevB EV93 main protease 3C with Rupintrivir (AG7088)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q3Y PDB entry 3Q3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.25 M MgCl2, 0.1 M Tris, 25% PEG 8k, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.995 α = 90 b = 63.911 β = 90.43 c = 66.357 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 CCD MARMOSAIC 225 mm CCD MIRRORS 2011-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.872600 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 30 100 52513 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.55 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 3Q3Y 1.5 30 49523 49523 2658 99.98 0.16745 0.16745 0.16581 0.1692 0.19796 0.2016 RANDOM 16.921
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] -0.24 0.07 0.72 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.196 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 11.828 r_dihedral_angle_1_deg 5.905 r_scangle_it 3.733 r_scbond_it 2.325 r_angle_refined_deg 1.409 r_mcangle_it 1.028 r_mcbond_it 0.528 r_chiral_restr 0.088
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.196 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 11.828 r_dihedral_angle_1_deg 5.905 r_scangle_it 3.733 r_scbond_it 2.325 r_angle_refined_deg 1.409 r_mcangle_it 1.028 r_mcbond_it 0.528 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2842 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 89
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling