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Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EK9 PDB ENTRY 1EK9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10.5 PROTEIN WAS CRYSTALLIZED FROM 0.1M CAPS PH10.5, 30% PEG400
Crystal Properties Matthews coefficient Solvent content 3.83 67.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.284 α = 90 b = 136.176 β = 90 c = 136.133 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 CCD MARRESEARCH SLITS 2007-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 3.2 22.1 97.7 0.15 9.53 5 36034 2.4
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 3.2 3.3 98.3 0.42 2.45 5
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 1EK9 3.2 22.08 36034 1906 96.7 0.268 0.266 0.2632 0.315 0.309 RANDOM 67.82
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] 0.15 0.06 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.674 r_dihedral_angle_3_deg 18.905 r_dihedral_angle_4_deg 16.988 r_dihedral_angle_1_deg 5.255 r_angle_refined_deg 1.033 r_scangle_it 0.828 r_mcangle_it 0.622 r_scbond_it 0.466 r_mcbond_it 0.341 r_nbtor_refined 0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.674 r_dihedral_angle_3_deg 18.905 r_dihedral_angle_4_deg 16.988 r_dihedral_angle_1_deg 5.255 r_angle_refined_deg 1.033 r_scangle_it 0.828 r_mcangle_it 0.622 r_scbond_it 0.466 r_mcbond_it 0.341 r_nbtor_refined 0.291 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.135 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_refined 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 9909 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing