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Asymmetric structure of trimeric AcrB from Escherichia coli
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 4.6 290 5 % polyethylene glycol 400, 16-22 % polyethylene glycol
300, 8-11 % glycerol, 70 mM Nacitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 4.60
Crystal Properties Matthews coefficient Solvent content 3.49 64.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.33 α = 103.9 b = 134.87 β = 94.64 c = 140.84 γ = 90.11
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 QUANTUM 210 2005-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 29.8 99.9 0.134 8.4 4.2 181133 -3
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 3.1 99.9 0.763 1.9 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IWG 3 29.8 172056 181137 9081 99.9 0.234 0.231 0.274 0.2876 RANDOM 51.41
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] 0.01 -0.01 -0.19 -0.08 0.08 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_3_deg 19.001 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_1_deg 5.092 r_angle_refined_deg 1.059 r_scangle_it 0.744 r_scbond_it 0.432 r_mcangle_it 0.354 r_nbtor_refined 0.3 r_nbd_refined 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_3_deg 19.001 r_dihedral_angle_4_deg 17.818 r_dihedral_angle_1_deg 5.092 r_angle_refined_deg 1.059 r_scangle_it 0.744 r_scbond_it 0.432 r_mcangle_it 0.354 r_nbtor_refined 0.3 r_nbd_refined 0.197 r_mcbond_it 0.197 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.121 r_symmetry_hbond_refined 0.08 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47046 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 52
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling