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Conformation of the AcrB Multidrug Efflux Pump in Mutants of the Putative Proton Relay Pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T9U PDB ENTRY 1T9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.57 73.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.035 α = 90 b = 145.035 β = 90 c = 513.672 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 QUANTUM 315 2005-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.65 50 94.7 585851 1.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.65 3.78 92.3
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 1T9U 3.65 20 20020 1093 90 0.263 0.261 0.3691 0.303 0.3974 RANDOM 100.25
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] -1.41 -0.71 -1.41 2.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.712 r_dihedral_angle_3_deg 30.609 r_dihedral_angle_1_deg 24.182 r_dihedral_angle_4_deg 22.458 r_scangle_it 9.972 r_scbond_it 6.939 r_angle_refined_deg 6.585 r_mcangle_it 4.504 r_mcbond_it 3.036 r_nbd_refined 0.514
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.712 r_dihedral_angle_3_deg 30.609 r_dihedral_angle_1_deg 24.182 r_dihedral_angle_4_deg 22.458 r_scangle_it 9.972 r_scbond_it 6.939 r_angle_refined_deg 6.585 r_mcangle_it 4.504 r_mcbond_it 3.036 r_nbd_refined 0.514 r_symmetry_vdw_refined 0.503 r_chiral_restr 0.484 r_xyhbond_nbd_refined 0.46 r_nbtor_refined 0.429 r_symmetry_hbond_refined 0.429 r_bond_refined_d 0.091 r_gen_planes_refined 0.021 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 7718 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling