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Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 4.3
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 NaCl, MES
Crystal Properties Matthews coefficient Solvent content 2.81 56.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.593 α = 90 b = 87.428 β = 90 c = 46.328 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 293 IMAGE PLATE RIGAKU RAXIS IV++ OSMIC VARIMAX 2014-11-08 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE MAATEL IMAGINE ELLIPTICAL MIRRORS 2014-12-04 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.540 2 NUCLEAR REACTOR ORNL High Flux Isotope Reactor BEAMLINE CG4D 2.8-4.0 ORNL High Flux Isotope Reactor CG4D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 1.75 40 86.2 34 4.3 21726
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1.75 33.74 25099 19201 949 76.5 0.203 0.1931 0.218 0.2046 27.64 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.3 36.58 11249 7848 337 69.8 0.212 0.224 27.64
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 x_torsion_deg 18.9 x_torsion_deg 18.9 x_angle_deg 1.1 x_angle_deg 1.1 x_torsion_impr_deg 0.96 x_torsion_impr_deg 0.96 x_bond_d 0.009 x_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 38
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling PHASER phasing nCNS refinement LAUEGEN data reduction LSCALE data scaling