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Crystal Structure of wild-type HIV-1 Protease in complex with kd20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 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 41.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.761 α = 90 b = 57.791 β = 90 c = 62.017 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 2008-01-07 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 1.85 50 99.5 0.086 9.3 5.7 16110
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 1.85 1.92 95.1 0.421 3
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 ? 1.85 42.3 15262 805 99.22 0.177 0.17457 0.188 0.2243 0.2353 RANDOM 20.921
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] -0.68 0.2 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.813 r_dihedral_angle_4_deg 19.408 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_1_deg 6.287 r_scangle_it 2.086 r_angle_refined_deg 1.577 r_scbond_it 1.55 r_mcangle_it 1.012 r_angle_other_deg 0.877 r_mcbond_it 0.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.813 r_dihedral_angle_4_deg 19.408 r_dihedral_angle_3_deg 12.912 r_dihedral_angle_1_deg 6.287 r_scangle_it 2.086 r_angle_refined_deg 1.577 r_scbond_it 1.55 r_mcangle_it 1.012 r_angle_other_deg 0.877 r_mcbond_it 0.733 r_nbd_other 0.206 r_symmetry_vdw_refined 0.204 r_mcbond_other 0.184 r_nbd_refined 0.178 r_symmetry_vdw_other 0.174 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.093 r_nbtor_other 0.087 r_bond_refined_d 0.009 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_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 122 Heterogen Atoms 41
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction AMoRE phasing