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X-ray structure of D25N chemical analogue of HIV-1 protease complexed with ketomethylene isostere inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HVP PDB ENTRY 4HVP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1M CITRATE, 0.2M SODIUM PHOPHATE, 30% (W/V) AMMONIUM SULFATE, 10% (V/V) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.028 α = 90 b = 58.551 β = 90 c = 61.584 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 110 CCD MARMOSAIC 300 mm CCD Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry 2007-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 1.8 50 99.2 0.089 0.07 31.3 7.8 17570 17428 7.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 98.6 0.59 0.495 3.9 7.9 1708
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4HVP 1.8 20 17373 882 98.61 0.196 0.194 0.1945 0.223 0.2239 RANDOM 24.053
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] -1.47 1.78 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.584 r_dihedral_angle_4_deg 22.4 r_dihedral_angle_3_deg 14.153 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.185 r_scbond_it 2.514 r_mcangle_it 1.648 r_angle_refined_deg 1.595 r_mcbond_it 1.048 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.584 r_dihedral_angle_4_deg 22.4 r_dihedral_angle_3_deg 14.153 r_dihedral_angle_1_deg 5.954 r_scangle_it 4.185 r_scbond_it 2.514 r_mcangle_it 1.648 r_angle_refined_deg 1.595 r_mcbond_it 1.048 r_nbtor_refined 0.314 r_nbd_refined 0.257 r_symmetry_hbond_refined 0.187 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 55
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction