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Crystal structure of wild-type HIV-1 protease in complex with AF71
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 HANGING DROP, VAPOR DIFFUSION 6.2 295 24-29% ammonium sulfate, 63 mM sodium citrate, 126 mM phosphate buffer, pH 6.2, HANGING DROP, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.11 41.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.772 α = 90 b = 58.377 β = 90 c = 61.742 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 100 IMAGE PLATE RIGAKU RAXIS IV 2009-06-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 50 96.9 0.058 14.2 5 18541
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.81 92 0.377 4 1741
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 PDB ENTRY 1F7A 1.75 42.42 18509 954 96.9 0.1705 0.1692 0.1807 0.1944 0.2035 RANDOM 26.9575
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] -0.77 0.13 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.198 r_dihedral_angle_4_deg 16.592 r_dihedral_angle_3_deg 10.017 r_dihedral_angle_1_deg 6.29 r_scangle_it 1.973 r_angle_refined_deg 1.449 r_scbond_it 1.213 r_angle_other_deg 0.773 r_mcangle_it 0.75 r_mcbond_it 0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.198 r_dihedral_angle_4_deg 16.592 r_dihedral_angle_3_deg 10.017 r_dihedral_angle_1_deg 6.29 r_scangle_it 1.973 r_angle_refined_deg 1.449 r_scbond_it 1.213 r_angle_other_deg 0.773 r_mcangle_it 0.75 r_mcbond_it 0.409 r_mcbond_other 0.104 r_chiral_restr 0.073 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1498 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 50
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing