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Crystal structure of HIV-1 protease inhibitor, KC32 complexed with wild-type protease
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 VAPOR DIFFUSION, HANGING DROP 6.2 298 126 mM sodium phosphate pH6.2, 63mM sodium citrate, 24%-29% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 41.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.79 α = 90 b = 58.245 β = 90 c = 62.014 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 osmics mirrors 2007-08-01 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) 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 1.85 50 98.4 0.087 8.9 6.3 16073
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1F7A 1.85 39.28 15216 15216 810 98.37 0.18248 0.18037 0.1871 0.22327 0.2319 RANDOM 18.6
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] -0.58 -0.04 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.631 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 10.734 r_dihedral_angle_1_deg 6.163 r_scangle_it 1.811 r_angle_refined_deg 1.317 r_scbond_it 1.193 r_angle_other_deg 0.816 r_mcangle_it 0.768 r_mcbond_it 0.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.631 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 10.734 r_dihedral_angle_1_deg 6.163 r_scangle_it 1.811 r_angle_refined_deg 1.317 r_scbond_it 1.193 r_angle_other_deg 0.816 r_mcangle_it 0.768 r_mcbond_it 0.548 r_symmetry_vdw_other 0.252 r_symmetry_vdw_refined 0.24 r_symmetry_hbond_refined 0.203 r_nbd_other 0.194 r_nbd_refined 0.19 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.127 r_mcbond_other 0.127 r_chiral_restr 0.084 r_nbtor_other 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1490 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing