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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 VAPOR DIFFUSION 4.6 290 5% PEG 400, 16-22% PEG 300, 8-11% glycerol, 70mM sodium citrate, pH 4.6, VAPOR DIFFUSION, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.46 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 222.8 α = 90 b = 134.1 β = 98.21 c = 161.01 γ = 90
Symmetry Space Group C 1 2 1
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 MARRESEARCH 2005-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 2.9 30 99.3 0.073 13.4 4.2 103912 103134 1 1
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 2.9 3.08 97 0.956 1.6 4.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1IWG 2.9 29.51 98361 98361 5177 99.77 0.22761 0.22551 0.2263 0.26677 0.2649 RANDOM 73.945
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] 6.21 4.25 -3.26 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.386 r_dihedral_angle_3_deg 18.854 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_1_deg 5.148 r_angle_refined_deg 1.061 r_scangle_it 0.783 r_scbond_it 0.457 r_mcangle_it 0.35 r_nbtor_refined 0.301 r_nbd_refined 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.386 r_dihedral_angle_3_deg 18.854 r_dihedral_angle_4_deg 16.575 r_dihedral_angle_1_deg 5.148 r_angle_refined_deg 1.061 r_scangle_it 0.783 r_scbond_it 0.457 r_mcangle_it 0.35 r_nbtor_refined 0.301 r_nbd_refined 0.198 r_mcbond_it 0.194 r_symmetry_vdw_refined 0.137 r_xyhbond_nbd_refined 0.118 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.069 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 23624 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data scaling MOLREP phasing