☰ Navigation Tabs
HIV Protease with fragment 4D9 bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AZ8 Dimer generated from PDB entry 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 277.0K
Crystal Properties Matthews coefficient Solvent content 2.74 55.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.518 α = 90 b = 85.91 β = 90 c = 46.44 γ = 90
Symmetry Space Group P 21 21 2
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 MAR scanner 345 mm plate Monochromator:Side scattering bent cube-root I-beam single crystal; asymmetric
cut 4.965 degs; Mirrors: Rh coated flat mirror 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97945 SSRL BL11-1
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 1.8 31.53 95.2 0.064 0.064 5.5 3.3 22686 21597 23.1
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 1.8 1.85 75.4 0.183 0.183 3.8 2.1 3398
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 Dimer generated from PDB entry 2AZ8 1.8 31.53 21566 1106 95.2 0.208 0.206 0.2022 0.246 0.2406 RANDOM 27.867
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] 2.82 -1.75 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.324 r_dihedral_angle_4_deg 13.615 r_dihedral_angle_3_deg 11.346 r_dihedral_angle_1_deg 5.336 r_scangle_it 3.36 r_scbond_it 1.932 r_mcangle_it 1.262 r_angle_refined_deg 1.064 r_mcbond_it 0.669 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.324 r_dihedral_angle_4_deg 13.615 r_dihedral_angle_3_deg 11.346 r_dihedral_angle_1_deg 5.336 r_scangle_it 3.36 r_scbond_it 1.932 r_mcangle_it 1.262 r_angle_refined_deg 1.064 r_mcbond_it 0.669 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection MOSFLM data reduction SCALA data scaling MOLREP phasing