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Crystal structure of protease inhibitor, KB60 in complex with wild type HIV-1 protease
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.2 298 126 mM sodium phosphate pH 6.2, 63 mM sodium citrate, 24-29% ammonium sulphate, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.809 α = 90 b = 58.131 β = 90 c = 61.568 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 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 99.7 0.06 6.6 16121
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 1.85 1.92 97.4 0.319 4.7 1547
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.85 25.23 16079 808 99.57 0.172 0.169 0.221 0.2447 RANDOM 24.766
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] -0.76 -0.01 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.748 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_3_deg 10.141 r_dihedral_angle_1_deg 6.041 r_scangle_it 1.52 r_angle_refined_deg 1.403 r_scbond_it 0.997 r_mcangle_it 0.747 r_angle_other_deg 0.698 r_mcbond_it 0.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.748 r_dihedral_angle_4_deg 15.18 r_dihedral_angle_3_deg 10.141 r_dihedral_angle_1_deg 6.041 r_scangle_it 1.52 r_angle_refined_deg 1.403 r_scbond_it 0.997 r_mcangle_it 0.747 r_angle_other_deg 0.698 r_mcbond_it 0.527 r_symmetry_hbond_refined 0.204 r_nbd_other 0.18 r_nbd_refined 0.175 r_symmetry_vdw_other 0.167 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.132 r_mcbond_other 0.109 r_symmetry_vdw_refined 0.09 r_nbtor_other 0.079 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1486 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 65
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing