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Crystal structure of the Chitinase Domain of the Spore Coat Protein CotE from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6T9M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 Reservoir, 1 ml 0.1 M sodium malonate pH 5.5, 13% PEG 3,350 and 3 microlitres of pentaethylene glycol monooctyl ether (C8E5)
Drops contained 2 microlitres of protein at 20 mg/ml in 50 mM Tris-HCl, pH 7.5, 500 mM NaCl, 10 mM imidazole, a 3 microlitres of reservoir solution.
Crystal Properties Matthews coefficient Solvent content 3.89 68.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.076 α = 90 b = 82.076 β = 90 c = 325.883 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2017-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.17 81.41 100 1 9.5 18.3 35657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.17 0.64
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6T9M 2.1 54.373 39192 1918 99.957 0.219 0.2163 0.2163 0.2674 0.2675 54.348
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] -0.001 -0.001 -0.001 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.317 r_lrange_it 30.8 r_lrange_other 30.797 r_dihedral_angle_3_deg 15.81 r_dihedral_angle_4_deg 14.717 r_dihedral_angle_1_deg 7.483 r_scangle_it 7.218 r_scangle_other 7.216 r_mcangle_it 7.017 r_mcangle_other 7.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.317 r_lrange_it 30.8 r_lrange_other 30.797 r_dihedral_angle_3_deg 15.81 r_dihedral_angle_4_deg 14.717 r_dihedral_angle_1_deg 7.483 r_scangle_it 7.218 r_scangle_other 7.216 r_mcangle_it 7.017 r_mcangle_other 7.016 r_scbond_it 4.903 r_scbond_other 4.901 r_mcbond_it 4.847 r_mcbond_other 4.847 r_angle_other_deg 2.376 r_angle_refined_deg 1.64 r_symmetry_xyhbond_nbd_refined 0.338 r_xyhbond_nbd_refined 0.263 r_nbd_other 0.247 r_symmetry_nbd_other 0.221 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.175 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.071 r_bond_other_d 0.036 r_bond_refined_d 0.009 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2699 Nucleic Acid Atoms Solvent Atoms 138 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing