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HIV Protease (PR) with TL-3 in the active site and (Z)-N-(thiazol-2-yl)-N'-tosylcarbamimidate in the exosite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EJK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 298 1.3M NH4SO4, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.18 43.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.953 α = 90 b = 62.953 β = 90 c = 82.306 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 1 2012-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9794 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.701 32.846 99.8 0.053 0.057 0.022 16.3 6.4 20325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.701 1.79 98.9 1.635 1.635 1.84 0.828 0.5 4.8
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 4EJK 1.8 32.846 16309 861 99.94 0.1755 0.1735 0.1749 0.2142 0.2168 RANDOM 39.775
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] 0.06 0.03 0.06 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.421 r_sphericity_free 27.711 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_4_deg 12.778 r_sphericity_bonded 8.5 r_dihedral_angle_1_deg 7.17 r_mcangle_it 2.889 r_mcbond_other 2.48 r_mcbond_it 2.479 r_angle_refined_deg 1.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.421 r_sphericity_free 27.711 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_4_deg 12.778 r_sphericity_bonded 8.5 r_dihedral_angle_1_deg 7.17 r_mcangle_it 2.889 r_mcbond_other 2.48 r_mcbond_it 2.479 r_angle_refined_deg 1.854 r_rigid_bond_restr 1.208 r_angle_other_deg 0.992 r_chiral_restr 0.093 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 104
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing autoXDS data reduction