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HIV Protease (PR) dimer in closed form with TL-3 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 3KFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 2.4M NaFormate, 10% DMSO, pH4.6 NaOAc
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.916 α = 90 b = 66.295 β = 90 c = 92.175 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 2011-01-05 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 2.195 53.82 98.3 10.02 3.6 9437
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 2.195 2.24 0.34 2.29 1.73
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 3KFR 2.195 31.19 9437 451 98.36 0.1871 0.1837 0.1918 0.2595 0.2595 RANDOM 19.2
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] 0.01 0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.285 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 14.938 r_dihedral_angle_1_deg 7.264 r_mcangle_it 2.412 r_angle_refined_deg 1.948 r_mcbond_other 1.489 r_mcbond_it 1.488 r_angle_other_deg 1.377 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.285 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 14.938 r_dihedral_angle_1_deg 7.264 r_mcangle_it 2.412 r_angle_refined_deg 1.948 r_mcbond_other 1.489 r_mcbond_it 1.488 r_angle_other_deg 1.377 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1516 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 89
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing PROTEUM data reduction