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Crystal structure of AD-81 complexed 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, HANGING DROP 6.2 298 126mM sodium phosphate pH 6.2, 63mM sodium citrate, 27% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.778 α = 90 b = 58.314 β = 90 c = 61.693 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 2006-02-17 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 1.95 50 95.3 0.047 0.047 11.6 4.9 13238
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.95 42.37 12549 664 95.39 0.16828 0.1658 0.1769 0.21588 0.2232 RANDOM 33.944
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] -0.73 -0.07 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.544 r_dihedral_angle_4_deg 15.218 r_dihedral_angle_3_deg 10.692 r_dihedral_angle_1_deg 6.973 r_scangle_it 2.269 r_scbond_it 1.623 r_angle_refined_deg 1.294 r_mcangle_it 1.088 r_mcbond_it 0.812 r_angle_other_deg 0.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.544 r_dihedral_angle_4_deg 15.218 r_dihedral_angle_3_deg 10.692 r_dihedral_angle_1_deg 6.973 r_scangle_it 2.269 r_scbond_it 1.623 r_angle_refined_deg 1.294 r_mcangle_it 1.088 r_mcbond_it 0.812 r_angle_other_deg 0.628 r_mcbond_other 0.205 r_nbd_other 0.187 r_nbd_refined 0.186 r_symmetry_vdw_other 0.18 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.169 r_symmetry_vdw_refined 0.137 r_symmetry_hbond_refined 0.117 r_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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_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 1494 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing