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The crystal structure of the TolB box of Colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 10000, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.691347 27.276892
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.955 α = 90 b = 40.174 β = 97.18 c = 80.868 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IV++ Mirror 2007-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.6 30 97.9 0.095 0.111 7.7 3.6 12220 16.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 96.6 0.347 0.405 3.7 3.7 1753
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 (All) 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 1C5K 2.6 30 12220 11636 583 97.97 0.193 0.19316 0.19005 0.1996 0.25685 0.2668 RANDOM 16.571
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] 0.31 0.1 1.35 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_dihedral_angle_4_deg 23.246 r_dihedral_angle_3_deg 20.753 r_dihedral_angle_1_deg 14.446 r_scangle_it 2.056 r_angle_refined_deg 1.774 r_scbond_it 1.315 r_mcangle_it 0.871 r_mcbond_it 0.468 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_dihedral_angle_4_deg 23.246 r_dihedral_angle_3_deg 20.753 r_dihedral_angle_1_deg 14.446 r_scangle_it 2.056 r_angle_refined_deg 1.774 r_scbond_it 1.315 r_mcangle_it 0.871 r_mcbond_it 0.468 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.231 r_chiral_restr 0.193 r_xyhbond_nbd_refined 0.175 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 3089 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 8
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling