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Crystal structure of protease inhibitor, KB62 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 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.831 α = 90 b = 58.342 β = 90 c = 61.629 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 1.8 50 98.4 0.056 6 17324
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 1.8 1.86 86.1 0.339 3.5 1482
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1.8 25.3 17282 875 98.41 0.171 0.17 0.1835 0.194 0.2107 RANDOM 34.524
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] -0.29 -0.34 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.511 r_dihedral_angle_4_deg 14.819 r_dihedral_angle_3_deg 9.908 r_dihedral_angle_1_deg 6.138 r_scangle_it 1.468 r_angle_refined_deg 1.356 r_scbond_it 0.997 r_mcangle_it 0.731 r_angle_other_deg 0.677 r_mcbond_it 0.502
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.511 r_dihedral_angle_4_deg 14.819 r_dihedral_angle_3_deg 9.908 r_dihedral_angle_1_deg 6.138 r_scangle_it 1.468 r_angle_refined_deg 1.356 r_scbond_it 0.997 r_mcangle_it 0.731 r_angle_other_deg 0.677 r_mcbond_it 0.502 r_symmetry_vdw_other 0.178 r_nbd_refined 0.174 r_nbd_other 0.173 r_nbtor_refined 0.165 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.127 r_mcbond_other 0.101 r_nbtor_other 0.079 r_chiral_restr 0.074 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 1498 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 51
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing