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Structure of TolB in complex with a peptide of the colicin E9 T- domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C5K PDB ENTRY 1C5K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 24% POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, 80 MM CACL2, 100 MM HEPES, PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.092 α = 90 b = 39.933 β = 110.62 c = 154.848 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 100 CCD MARRESEARCH 2006-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2 144 100 0.14 14.1 6.3 102162 2
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 2.05 100 0.4 6.3 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1C5K 2 144.34 97047 5100 100 0.17 0.168 0.222 0.227 RANDOM 15.76
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] -0.68 -1.06 0.02 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.419 r_dihedral_angle_4_deg 15.356 r_dihedral_angle_3_deg 11.3 r_dihedral_angle_1_deg 4.362 r_scangle_it 3.505 r_scbond_it 2.261 r_angle_refined_deg 1.515 r_mcangle_it 1.47 r_mcbond_it 0.907 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.419 r_dihedral_angle_4_deg 15.356 r_dihedral_angle_3_deg 11.3 r_dihedral_angle_1_deg 4.362 r_scangle_it 3.505 r_scbond_it 2.261 r_angle_refined_deg 1.515 r_mcangle_it 1.47 r_mcbond_it 0.907 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.165 r_symmetry_vdw_refined 0.153 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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_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 12269 Nucleic Acid Atoms Solvent Atoms 1242 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling MOLREP phasing