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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, HANGING DROP 7.5 293.5 Precipitant: 0.1M sodium chloride, 0.1M sodium HEPES pH7.5, 12% w/v PEG 4000, 0.5 microliter 8mg/ml colicin Ib C domain mix with the same volume precipitant in the drop
colicin Ib C domain buffer:20mM sodium, citrate pH5.2, 200mM NaCl
Crystal Properties Matthews coefficient Solvent content 5.26 76.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.994 α = 90 b = 91.994 β = 90 c = 113.896 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 RAYONIX MX300-HS 2021-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1 NSRRC BL15A1
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) 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 2.94 30 99.9 0.09 0.053 0.101 0.047 9 4.6 11058 11040 54.03
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) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.94 3.06 100 0.556 0.399 0.627 0.289 0.925 4.7
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 26.08 1.34 9151 904 96.23 0.1985 0.1962 0.1974 0.2189 0.2192 49.3
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 13.3337 f_angle_d 0.5439 f_chiral_restr 0.0406 f_plane_restr 0.0032 f_bond_d 0.0029
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 collection HKL-2000 data scaling PHENIX model building