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The structure of the efflux pump AcrB in complex with bile acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IWG PDB ENTRY 1IWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 10% PEG 4000, 0.1 M HEPES PH 7.5, 0.1 M AMMONIUM SULPHATE AND 22% V/V GLYCEROL
Crystal Properties Matthews coefficient Solvent content 4.64 73.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.49 α = 90 b = 145.49 β = 90 c = 515.181 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC CCD MIRRORS 2007-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 3.85 57.45 96.4 0.23 2.5 4.1 19539
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 3.85 4.02 96.2 0.56 1.3 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IWG 3.85 40 18545 980 95.74 0.28141 0.27779 0.2695 0.34919 0.332 RANDOM 75.719
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] 1.49 0.74 1.49 -2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.247 r_dihedral_angle_3_deg 21.645 r_dihedral_angle_4_deg 18.709 r_dihedral_angle_1_deg 6.566 r_angle_refined_deg 1.392 r_scangle_it 0.855 r_mcangle_it 0.628 r_scbond_it 0.507 r_mcbond_it 0.346 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.247 r_dihedral_angle_3_deg 21.645 r_dihedral_angle_4_deg 18.709 r_dihedral_angle_1_deg 6.566 r_angle_refined_deg 1.392 r_scangle_it 0.855 r_mcangle_it 0.628 r_scbond_it 0.507 r_mcbond_it 0.346 r_nbtor_refined 0.312 r_nbd_refined 0.247 r_symmetry_vdw_refined 0.221 r_symmetry_hbond_refined 0.197 r_xyhbond_nbd_refined 0.179 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7841 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing