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Porcine pepsin in complex with saquinavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 2.9 295 2 M Ammonium Chloride, 0.1 M acetic acid
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.39 α = 90 b = 66.39 β = 90 c = 284.572 γ = 120
Symmetry Space Group P 65 2 2
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 300 mm CCD 2019-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.89 57.5 97.8 0.091 0.11 0.054 0.995 7.9 5.5 30114
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 1.89 1.93 98 0.73 0.85 0.42 0.649 1.6 5.9
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 4PEP 1.89 53.36 28530 1544 97.01 0.17978 0.17762 0.1899 0.21975 0.2267 RANDOM 38.382
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] 0.1 0.05 0.1 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.302 r_dihedral_angle_3_deg 13.197 r_dihedral_angle_1_deg 6.846 r_long_range_B_refined 5.419 r_long_range_B_other 5.297 r_dihedral_angle_4_deg 3.72 r_scangle_other 2.795 r_mcangle_other 2.359 r_mcangle_it 2.338 r_scbond_it 1.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.302 r_dihedral_angle_3_deg 13.197 r_dihedral_angle_1_deg 6.846 r_long_range_B_refined 5.419 r_long_range_B_other 5.297 r_dihedral_angle_4_deg 3.72 r_scangle_other 2.795 r_mcangle_other 2.359 r_mcangle_it 2.338 r_scbond_it 1.723 r_scbond_other 1.723 r_angle_refined_deg 1.663 r_mcbond_it 1.433 r_mcbond_other 1.369 r_angle_other_deg 1.166 r_chiral_restr 0.107 r_bond_refined_d 0.014 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 2433 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 49
Software Software Software Name Purpose PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing PHENIX refinement