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Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.48 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.01 α = 90 b = 95.797 β = 90 c = 112.915 γ = 90
Symmetry Space Group P 21 21 21
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 2004-03-13 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.2 30 99.8 0.06 14.9 3.8 66915
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 2.29 99.9 0.29 4.6 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT 2.2 30 34239 1117 99.8 0.198 0.197 0.1985 0.244 0.247 RANDOM 41.66
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] 4.04 -1.01 -3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.036 r_dihedral_angle_3_deg 16.159 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_1_deg 5.95 r_scangle_it 2.846 r_scbond_it 1.819 r_angle_refined_deg 1.4 r_mcangle_it 1.116 r_mcbond_it 0.673 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.036 r_dihedral_angle_3_deg 16.159 r_dihedral_angle_4_deg 15.544 r_dihedral_angle_1_deg 5.95 r_scangle_it 2.846 r_scbond_it 1.819 r_angle_refined_deg 1.4 r_mcangle_it 1.116 r_mcbond_it 0.673 r_nbtor_refined 0.307 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.199 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.091 r_bond_refined_d 0.012 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 4433 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling