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Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLN-THR-PHE*TYR-VAL-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 bound with TMC114
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 126mM sodium phosphate pH 6.2; 63mM sodium citrate; 25-35% Ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.03 39.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.074 α = 90 b = 58.535 β = 90 c = 61.711 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 2005-03-31 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 2.25 42.49 91 0.065 0.065 10.3 3.5 8523 8523
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 bound with TMC114 2.25 42.49 8037 8037 405 91.66 0.18977 0.18977 0.18702 0.24386 RANDOM 59.773
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] -2.47 1.91 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.553 r_dihedral_angle_3_deg 15.778 r_dihedral_angle_4_deg 9.234 r_dihedral_angle_1_deg 7.224 r_scangle_it 3.141 r_scbond_it 2.147 r_mcangle_it 1.378 r_angle_refined_deg 1.264 r_mcbond_it 0.946 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.553 r_dihedral_angle_3_deg 15.778 r_dihedral_angle_4_deg 9.234 r_dihedral_angle_1_deg 7.224 r_scangle_it 3.141 r_scbond_it 2.147 r_mcangle_it 1.378 r_angle_refined_deg 1.264 r_mcbond_it 0.946 r_nbtor_refined 0.314 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.088 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1542 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling