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Crystal Structure of wild type HIV-1 protease in complex with CARB-AD37
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 6.2 298 126mM Sodium Phosphate, 63mM sodium citrate, 24-29% ammonium sulphate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.08 40.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.647 α = 90 b = 57.638 β = 90 c = 61.775 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 200 IMAGE PLATE RIGAKU RAXIS IV osmic mirrors 2005-12-29 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 1.93 50 99.4 0.065 6.5 8.5 6.6 14044
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 (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 1F7A 1.93 42.14 13301 701 99.27 0.16241 0.16241 0.16058 0.1719 0.19839 0.2157 RANDOM 17.387
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] -0.65 -0.19 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.266 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 6.24 r_scangle_it 1.627 r_angle_refined_deg 1.221 r_scbond_it 1.06 r_angle_other_deg 0.838 r_mcangle_it 0.705 r_mcbond_it 0.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.266 r_dihedral_angle_4_deg 16.979 r_dihedral_angle_3_deg 11.148 r_dihedral_angle_1_deg 6.24 r_scangle_it 1.627 r_angle_refined_deg 1.221 r_scbond_it 1.06 r_angle_other_deg 0.838 r_mcangle_it 0.705 r_mcbond_it 0.494 r_nbd_other 0.178 r_nbd_refined 0.176 r_symmetry_vdw_other 0.17 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.116 r_mcbond_other 0.111 r_symmetry_vdw_refined 0.108 r_nbtor_other 0.08 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1486 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing