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Crystal structure of I50L/A71V mutant of hiv-1 protease in complex with inhibitor darunavir
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 6.2 300 pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.14 α = 90 b = 57.891 β = 90 c = 61.364 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 Yale Mirrors 2004-03-28 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 2.1 50 96.6 0.092 11.443 3.2 10762
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 2.1 2.18 95.6 0.461 1027
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1F7A 2.1 42.26 10740 507 96.79 0.188 0.186 0.24 0.25 RANDOM 6.32
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] -0.4 -0.46 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.145 r_dihedral_angle_4_deg 14.465 r_dihedral_angle_3_deg 13.456 r_dihedral_angle_1_deg 6.315 r_angle_refined_deg 1.151 r_scangle_it 1.056 r_angle_other_deg 0.825 r_scbond_it 0.722 r_mcangle_it 0.485 r_mcbond_it 0.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.145 r_dihedral_angle_4_deg 14.465 r_dihedral_angle_3_deg 13.456 r_dihedral_angle_1_deg 6.315 r_angle_refined_deg 1.151 r_scangle_it 1.056 r_angle_other_deg 0.825 r_scbond_it 0.722 r_mcangle_it 0.485 r_mcbond_it 0.439 r_symmetry_vdw_other 0.197 r_nbd_other 0.182 r_symmetry_hbond_refined 0.18 r_nbd_refined 0.178 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.151 r_nbtor_other 0.082 r_chiral_restr 0.067 r_mcbond_other 0.062 r_gen_planes_other 0.007 r_gen_planes_refined 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1458 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 75
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing