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Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease (D30N/N88D) in Complex with the p1-p6 substrate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3R PDB entry 1T3R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 28% PEG 5000, 0.1M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.02 39.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.672 α = 90 b = 60.114 β = 99.09 c = 60.196 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm Mirrors 2009-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.033 APS 14-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.78 50 99.2 0.068 14.7 3.9 34288 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.86 99.7 0.355 3.88 3.7
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 1T3R 1.78 50 32455 1711 97.75 0.20312 0.20039 0.2135 0.25461 0.2616 RANDOM 29.977
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] -2.56 -0.48 0.83 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.162 r_dihedral_angle_4_deg 14.942 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 7.449 r_scangle_it 5.048 r_scbond_it 3.235 r_mcangle_it 2.184 r_angle_refined_deg 1.404 r_mcbond_it 1.335 r_angle_other_deg 0.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.162 r_dihedral_angle_4_deg 14.942 r_dihedral_angle_3_deg 14.528 r_dihedral_angle_1_deg 7.449 r_scangle_it 5.048 r_scbond_it 3.235 r_mcangle_it 2.184 r_angle_refined_deg 1.404 r_mcbond_it 1.335 r_angle_other_deg 0.783 r_mcbond_other 0.411 r_chiral_restr 0.088 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.001 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3060 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction BioCARS-developed data collection HKL-2000 data reduction HKL-2000 data scaling