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Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 6.0
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 2.82 56.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.724 α = 90 b = 87.257 β = 90 c = 46.547 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 2014-08-20 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE MAATEL IMAGINE COLLIMATORS 2014-10-13 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.540 2 NUCLEAR REACTOR LADI/ILL 2.80 - 4.0
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 98.2 0.048 26.5 3.9 21102 2 2 27.61 83.5 0.147 5.2 5.9 13170
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) 1.85 1.92 0.478 2.8 3.9 2 2 2.11 0.267 3.2 5.2
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 20 2.5 21426 18339 926 87.9 0.194 0.1837 0.201 0.1926 RANDOM 27.3 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 40 2.5 16128 11729 564 68.8 0.217 0.245 RANDOM 27.3
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 c_torsion_deg 16.4 c_torsion_deg 16.4 c_angle_deg 1 c_angle_deg 1 c_torsion_impr_deg 0.85 c_torsion_impr_deg 0.85 c_bond_d 0.008 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 116 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