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Crystal structure of HIV-1 protease inhibitor KC53 in complex 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 6.2 298 126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.674 α = 90 b = 57.858 β = 90 c = 61.914 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 2007-03-28 M 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) 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 1.95 50 99.7 0.102 0.102 8.3 6.6 13809
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 1.95 39.22 13080 13080 689 99.57 0.16677 0.16497 0.1783 0.20087 0.2084 RANDOM 21.641
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] -0.39 0.21 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.759 r_dihedral_angle_4_deg 19.619 r_dihedral_angle_3_deg 11.223 r_dihedral_angle_1_deg 6.05 r_scangle_it 1.509 r_angle_refined_deg 1.34 r_scbond_it 1.015 r_angle_other_deg 0.711 r_mcangle_it 0.71 r_mcbond_it 0.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.759 r_dihedral_angle_4_deg 19.619 r_dihedral_angle_3_deg 11.223 r_dihedral_angle_1_deg 6.05 r_scangle_it 1.509 r_angle_refined_deg 1.34 r_scbond_it 1.015 r_angle_other_deg 0.711 r_mcangle_it 0.71 r_mcbond_it 0.494 r_symmetry_vdw_other 0.195 r_nbd_other 0.18 r_nbd_refined 0.178 r_nbtor_refined 0.166 r_symmetry_vdw_refined 0.146 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.119 r_mcbond_other 0.103 r_nbtor_other 0.081 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 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 1486 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing