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Structure of HIV-1 protease D25N complexed with rt-rh analogue peptide GLY-ALA-ASP-ILE-PHE*TYR-LEU-ASP-GLY-ALA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T3R 1T3R - Crystal structure of HIV-1 protease complexed with the inhibitor TMC114
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 126 mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35%Ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.171 α = 90 b = 57.692 β = 90 c = 61.482 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 2005-03-29 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) 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 2 42.07 92.7 0.034 0.034 21.2 5 11909 11909
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1T3R - Crystal structure of HIV-1 protease complexed with the inhibitor TMC114 2 42.07 11295 11295 586 92.82 0.1979 0.1979 0.19505 0.25737 RANDOM 46.962
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] -0.82 -0.8 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.513 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 14.756 r_dihedral_angle_1_deg 7.125 r_scangle_it 2.177 r_scbond_it 1.514 r_angle_refined_deg 1.218 r_mcangle_it 0.986 r_mcbond_it 0.786 r_angle_other_deg 0.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.513 r_dihedral_angle_4_deg 16.62 r_dihedral_angle_3_deg 14.756 r_dihedral_angle_1_deg 7.125 r_scangle_it 2.177 r_scbond_it 1.514 r_angle_refined_deg 1.218 r_mcangle_it 0.986 r_mcbond_it 0.786 r_angle_other_deg 0.678 r_symmetry_vdw_other 0.198 r_nbd_other 0.19 r_nbd_refined 0.188 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.167 r_mcbond_other 0.163 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.144 r_nbtor_other 0.081 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1540 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling