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Crystal Structure of wild-type HIV-1 Protease in complex with af60
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop, vapor diffusion 6.2 295 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.09 41.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.713 α = 90 b = 57.843 β = 90 c = 61.79 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 CCD ADSC QUANTUM 315 2008-11-07 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.5 50 99.7 0.045 13.1 5.7 29740
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 1.5 1.55 99.9 0.271 5.8 2907
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 ? 1.5 39.19 29687 1504 99.74 0.1686 0.167 0.177 0.1967 0.2024 RANDOM 18.572
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] -0.66 0.18 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.988 r_dihedral_angle_4_deg 10.764 r_dihedral_angle_3_deg 9.45 r_dihedral_angle_1_deg 6.177 r_scangle_it 2.453 r_scbond_it 1.735 r_angle_refined_deg 1.433 r_mcangle_it 1.056 r_angle_other_deg 0.838 r_mcbond_it 0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.988 r_dihedral_angle_4_deg 10.764 r_dihedral_angle_3_deg 9.45 r_dihedral_angle_1_deg 6.177 r_scangle_it 2.453 r_scbond_it 1.735 r_angle_refined_deg 1.433 r_mcangle_it 1.056 r_angle_other_deg 0.838 r_mcbond_it 0.818 r_nbd_other 0.202 r_symmetry_vdw_other 0.195 r_nbd_refined 0.182 r_mcbond_other 0.179 r_nbtor_refined 0.169 r_symmetry_vdw_refined 0.158 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.091 r_symmetry_hbond_refined 0.086 r_nbtor_other 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1498 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 64
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing