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Symmetric structure of E. coli AcrB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I6W PDB entry 2I6W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 293 0.1M MES, 31% PEG 400, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.62 73.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.74 α = 90 b = 145.74 β = 90 c = 514 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 2007-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97980 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.42 20 99.3 0.124 0.124 11.97 6.12 28788 3 67.7
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 3.42 3.6 100 0.619 3.25 6.24 4072
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 2I6W 3.42 19.97 28788 27636 1152 100 0.29114 0.28851 0.2824 0.35459 0.3436 RANDOM 44.522
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] 0.1 0.05 0.1 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.052 r_dihedral_angle_3_deg 18.867 r_dihedral_angle_4_deg 13.982 r_dihedral_angle_1_deg 8.433 r_angle_refined_deg 1.408 r_angle_other_deg 1.075 r_scangle_it 0.951 r_mcangle_it 0.698 r_mcbond_it 0.639 r_scbond_it 0.615
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.052 r_dihedral_angle_3_deg 18.867 r_dihedral_angle_4_deg 13.982 r_dihedral_angle_1_deg 8.433 r_angle_refined_deg 1.408 r_angle_other_deg 1.075 r_scangle_it 0.951 r_mcangle_it 0.698 r_mcbond_it 0.639 r_scbond_it 0.615 r_symmetry_vdw_refined 0.262 r_symmetry_vdw_other 0.262 r_nbd_refined 0.252 r_nbd_other 0.2 r_xyhbond_nbd_refined 0.194 r_chiral_restr 0.19 r_nbtor_refined 0.19 r_xyhbond_nbd_other 0.149 r_symmetry_hbond_refined 0.112 r_nbtor_other 0.088 r_mcbond_other 0.058 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7950 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling MOLREP phasing