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Crystal structure of AcrBZ in complex with antibiotic puromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 80 mM Bis-Tris, pH 6.0, 50 mM sodium citrate, 120 mM KCl, 10% PEG 4000, 0.5% N,N-dimethyldodecylamine N-oxide
Crystal Properties Matthews coefficient Solvent content 3.92 68.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.245 α = 90 b = 167.646 β = 90 c = 249.98 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 PIXEL DECTRIS PILATUS3 6M 2014-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9794 Diamond I24
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 3 50 92.5 0.175 5.2 3 94271
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4DX5 3.2 34.928 1.35 94200 4695 91.97 0.1859 0.1827 0.1861 0.2448 0.2442
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 17.204 f_angle_d 1.91 f_chiral_restr 0.112 f_bond_d 0.019 f_plane_restr 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26769 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 530
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction SCALEPACK data scaling PHASER phasing