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Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with amprenavir at pH 6.0
NEUTRON DIFFRACTION - X-RAY 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 290 1M NaCl, 0.1 M NaMES
Crystal Properties Matthews coefficient Solvent content 2.8 56.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.234 α = 90 b = 87.359 β = 90 c = 46.565 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 2016-03-03 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE MAATEL IMAGINE COLLIMATORS 2016-02-22 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54 2 NUCLEAR REACTOR LADI/ILL 2.8-4.0 LADI
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 1.85 40 95.9 0.046 26.1 4 20505 2 2.2 40 74.4 0.167 7.2 3.9 8933
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 0.465 2.7 4.1 2 2.2 2.32 0.308 4 3.4
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 1.85 36.61 2.5 21283 18040 885 84.8 0.191 0.1814 0.214 0.2086 RANDOM 27.93 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.2 33.76 2.5 12268 8394 397 65.6 0.217 0.255 RANDOM 27.93
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 15.3 x_torsion_deg 15.3 x_angle_deg 1.1 x_angle_deg 1.1 x_torsion_impr_deg 0.87 x_torsion_impr_deg 0.87 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 124 Heterogen Atoms 35
Software Software Software Name Purpose HKL-3000 data reduction HKL-3000 data scaling PHASER phasing nCNS refinement LAUEGEN data reduction LSCALE data scaling