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Crystal structure of wild-type inactive (D25N) HIV-1 protease complexed with wild-type HIV-1 NC-p1 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 6.2 298 126mM Sodium phosphate pH 6.2; 63mM sodium citrate; ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.06 α = 90 b = 57.369 β = 90 c = 61.302 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 Osmic Mirrors 2002-12-15 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 1.85 42 92.7 0.056 0.056 8.5 4 14812 14812
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 PDB ENTRY 1T3R 1.85 23 14812 13281 1503 100 0.19968 0.19968 0.19474 0.24308 RANDOM 27.948
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] -1.28 0.28 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.862 r_dihedral_angle_4_deg 14.145 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 6.733 r_scangle_it 1.861 r_scbond_it 1.395 r_angle_refined_deg 1.034 r_mcangle_it 0.749 r_mcbond_it 0.725 r_angle_other_deg 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.862 r_dihedral_angle_4_deg 14.145 r_dihedral_angle_3_deg 13.913 r_dihedral_angle_1_deg 6.733 r_scangle_it 1.861 r_scbond_it 1.395 r_angle_refined_deg 1.034 r_mcangle_it 0.749 r_mcbond_it 0.725 r_angle_other_deg 0.624 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.201 r_nbd_other 0.2 r_symmetry_vdw_other 0.199 r_nbtor_refined 0.173 r_mcbond_other 0.125 r_symmetry_hbond_refined 0.12 r_symmetry_vdw_refined 0.118 r_nbtor_other 0.084 r_chiral_restr 0.065 r_xyhbond_nbd_other 0.039 r_bond_refined_d 0.005 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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 1612 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing