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Structure of HIV-1 protease D25N complexed with the rt-rh analogue peptide GLY-ALA-GLU-VAL-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 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 sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2 38.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.861 α = 90 b = 57.5 β = 90 c = 61.887 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 2005-03-11 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 42.11 95.8 0.071 0.071 12.5 5 12332 12332
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 42.11 11693 11693 608 95.92 0.16307 0.16307 0.16035 0.216 RANDOM 37.719
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] 1.08 0.01 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.41 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_4_deg 12.352 r_dihedral_angle_1_deg 6.659 r_scangle_it 2.1 r_angle_refined_deg 1.455 r_scbond_it 1.411 r_mcangle_it 0.897 r_angle_other_deg 0.781 r_mcbond_it 0.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.41 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_4_deg 12.352 r_dihedral_angle_1_deg 6.659 r_scangle_it 2.1 r_angle_refined_deg 1.455 r_scbond_it 1.411 r_mcangle_it 0.897 r_angle_other_deg 0.781 r_mcbond_it 0.723 r_symmetry_vdw_other 0.206 r_nbd_refined 0.198 r_nbd_other 0.184 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.169 r_symmetry_hbond_refined 0.16 r_mcbond_other 0.152 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.087 r_nbtor_other 0.084 r_symmetry_hbond_other 0.05 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 1565 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 10
Software Software Software Name Purpose AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling