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HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AZ8 HIV PR dimer generated from monomer with TL-3 bound in 2AZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 277 0.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.01 38.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.72 α = 90 b = 65.57 β = 90 c = 92.36 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 CCD ADSC QUANTUM 315r Rh coated flat mirror 2008-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97946 SSRL BL7-1
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 1.15 25.3 97.8 0.051 0.051 6.7 3.8 63048 61661 12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.18 96.6 0.8 0.8 0.9 3.9 4432
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 HIV PR dimer generated from monomer with TL-3 bound in 2AZ8 1.3 25.3 42972 2151 98 0.184 0.183 0.182 0.207 0.2067 RANDOM 16.693
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] 0.09 -0.02 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 13.812 r_dihedral_angle_3_deg 10.527 r_dihedral_angle_1_deg 6.481 r_sphericity_free 4.003 r_scangle_it 3.801 r_sphericity_bonded 3.197 r_scbond_it 2.434 r_mcangle_it 1.928 r_angle_refined_deg 1.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.783 r_dihedral_angle_4_deg 13.812 r_dihedral_angle_3_deg 10.527 r_dihedral_angle_1_deg 6.481 r_sphericity_free 4.003 r_scangle_it 3.801 r_sphericity_bonded 3.197 r_scbond_it 2.434 r_mcangle_it 1.928 r_angle_refined_deg 1.437 r_rigid_bond_restr 1.29 r_mcbond_it 1.182 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1520 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing