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HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 2.4M NaFormate, 10% DMSO, pH4.5 NaOAc, 1.5% b-octyl glucoside
Crystal Properties Matthews coefficient Solvent content 1.98 37.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.548 α = 90 b = 65.273 β = 90 c = 91.503 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 APEX II CCD 2010-12-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.179 53.139 98.8 34.24 8.48 9352
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 2.18 2.22 80 0.43 3.9 4.1
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 4EJD 2.18 37.46 9352 450 98.81 0.1998 0.1963 0.2024 0.2722 0.2782 RANDOM 21.778
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.133 r_dihedral_angle_3_deg 14.125 r_dihedral_angle_4_deg 7.244 r_dihedral_angle_1_deg 7.092 r_mcangle_it 3.007 r_mcbond_it 1.756 r_mcbond_other 1.756 r_angle_refined_deg 1.641 r_angle_other_deg 0.847 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.133 r_dihedral_angle_3_deg 14.125 r_dihedral_angle_4_deg 7.244 r_dihedral_angle_1_deg 7.092 r_mcangle_it 3.007 r_mcbond_it 1.756 r_mcbond_other 1.756 r_angle_refined_deg 1.641 r_angle_other_deg 0.847 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1552 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 43
Software Software Software Name Purpose SCALA data scaling PDB_EXTRACT data extraction PHASER phasing REFMAC refinement