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Substrate envelope and drug resistance: crystal structure of r01 in complex with wild-type hiv-1 protease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F7A pdb entry 1F7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 298 0.126M Sodium Acetate; 0.063M Sodium citrate, 25-30% Ammonium sulphate, pH 5.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.873 α = 90 b = 58.167 β = 90 c = 61.653 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 100 IMAGE PLATE RIGAKU RAXIS IV Osmic Mirrors 2004-04-14 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) 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 1.599 42.26 99.9 0.028 19.2 5.7 24814 24814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.599 1.66 99.8 0.367
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 (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 1F7A 1.599 19.53 24814 23503 1261 99.83 0.16489 0.16312 0.1753 0.19667 0.2061 RANDOM 17.07
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] -0.62 0.11 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.644 r_dihedral_angle_4_deg 17.428 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 7.331 r_angle_other_deg 3.532 r_scangle_it 2.589 r_scbond_it 1.76 r_angle_refined_deg 1.43 r_mcangle_it 1.169 r_mcbond_it 0.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.644 r_dihedral_angle_4_deg 17.428 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_1_deg 7.331 r_angle_other_deg 3.532 r_scangle_it 2.589 r_scbond_it 1.76 r_angle_refined_deg 1.43 r_mcangle_it 1.169 r_mcbond_it 0.727 r_nbd_other 0.233 r_symmetry_hbond_refined 0.229 r_symmetry_vdw_other 0.227 r_nbd_refined 0.196 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.144 r_nbtor_other 0.111 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1827 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing