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Crystal structure of the carboxy-terminal channel-forming domain of Colicin Ib
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CII
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 1% Nucleosides mix (2% w/v Cytidine, 2% w/v Inosine, 2% w/v Ribavirin, 2% w/v Thymidine, 2% w/v Uridine)
0.1M Buffer system 1(Imidazole; MES
monohydrate (acid))
30% precipitant mix(40% v/v Glycerol; 20% w/v PEG 4000)
Crystal Properties Matthews coefficient Solvent content 5.06 75.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.742 α = 90 b = 90.742 β = 90 c = 113.391 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315r 2021-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 3.11 28.7 99.7 0.109 0.065 0.116 0.055 0.857 0.1 16.3 4.8 8332 35.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.21 98.7 0.904 0.426 0.712 0.356 0.769 0.03 2.4 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.11 28.7 1.36 8257 426 99.34 0.2002 0.1984 0.1987 0.2307 0.2307 70
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.8771 f_angle_d 0.909 f_chiral_restr 0.0465 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1529 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing