☰ Navigation Tabs
Crystal Structure of wild-type HIV-1 Protease in complex with kd13
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 6.2 295 126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 24-29% Ammonium Sulfate, hanging drop, vapor diffusion, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.1 41.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.774 α = 90 b = 57.885 β = 90 c = 61.752 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 YALE MIRRORS 2008-08-26 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.95 50 99.9 0.09 8.3 6.7 13796
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 1.95 2.02 99.8 0.414 5.7
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 39.22 13067 687 99.81 0.17909 0.17673 0.1859 0.2244 0.2321 RANDOM 22.71
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] -0.71 0.02 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.925 r_dihedral_angle_4_deg 17.232 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_1_deg 6.296 r_scangle_it 1.89 r_angle_refined_deg 1.431 r_scbond_it 1.293 r_angle_other_deg 0.84 r_mcangle_it 0.718 r_mcbond_it 0.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.925 r_dihedral_angle_4_deg 17.232 r_dihedral_angle_3_deg 11.934 r_dihedral_angle_1_deg 6.296 r_scangle_it 1.89 r_angle_refined_deg 1.431 r_scbond_it 1.293 r_angle_other_deg 0.84 r_mcangle_it 0.718 r_mcbond_it 0.531 r_nbd_refined 0.198 r_nbd_other 0.196 r_symmetry_hbond_refined 0.188 r_nbtor_refined 0.17 r_symmetry_vdw_refined 0.167 r_symmetry_vdw_other 0.145 r_xyhbond_nbd_refined 0.143 r_mcbond_other 0.141 r_nbtor_other 0.086 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 1486 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 53
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing