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Crystal structure of inhibitor saquinavir (SQV) in complex with multi-drug resistant HIV-1 protease (L63P/V82T/I84V) (referred to as ACT in paper)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A PDB ENTRY 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 300 pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.15 42.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.164 α = 90 b = 59.291 β = 90 c = 61.389 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 IMAGE PLATE RIGAKU RAXIS IV Yale Mirrors 2008-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2 42 97.2 0.07 0.07 6 6.6 12975 12975
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 THROUGHOUT PDB ENTRY 1F7A 2.2 20 9751 467 98.38 0.197 0.195 0.2006 0.246 0.2557 RANDOM 34.606
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] -1.14 -1.19 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.441 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 6.953 r_scangle_it 2.212 r_scbond_it 1.66 r_angle_refined_deg 1.273 r_mcbond_it 1.063 r_mcangle_it 1.022 r_angle_other_deg 0.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.441 r_dihedral_angle_4_deg 14.06 r_dihedral_angle_3_deg 13.593 r_dihedral_angle_1_deg 6.953 r_scangle_it 2.212 r_scbond_it 1.66 r_angle_refined_deg 1.273 r_mcbond_it 1.063 r_mcangle_it 1.022 r_angle_other_deg 0.714 r_nbd_other 0.205 r_nbd_refined 0.179 r_nbtor_refined 0.169 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_other 0.147 r_mcbond_other 0.124 r_nbtor_other 0.087 r_chiral_restr 0.077 r_symmetry_hbond_refined 0.072 r_xyhbond_nbd_other 0.032 r_bond_refined_d 0.008 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1477 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing