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X-ray crystal structure of bPI-11 hiv-1 protease complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 50mM sodium acetate buffer (pH 5.0), 20% saturated ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.68 54.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.302 α = 90 b = 86.01 β = 90 c = 46.549 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 95 PIXEL DECTRIS PILATUS3 6M 2018-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 46.6 99.8 0.043 29.3 6.2 126583
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 1 1.04 98.4 0.293 2.8 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FOURIER SYNTHESIS FREE R-VALUE 3FX5 1 43.005 1.38 126508 6326 99.77 0.1325 0.1316 0.1375 0.1501 0.1565 Random selection
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.146 f_angle_d 1.337 f_chiral_restr 0.075 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1512 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 90
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing