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Crystal structure of the catalytic domain of toxin B from Clostridium difficile in complex with UDP, Glc and manganese ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BV1 PDB ENTRY 2BV1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.85 56.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.777 α = 90 b = 97.298 β = 90 c = 114.448 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 2003-11-14 M SINGLE WAVELENGTH
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 2.55 30 99.9 0.06 20.5 7.3 24594
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 2.55 2.61 100 0.48 4.4 7.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BV1 2.55 20 23770 769 100 0.2 0.199 0.1998 0.245 0.2462 RANDOM 55.74
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] -1.42 -0.99 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.094 r_dihedral_angle_3_deg 15.755 r_dihedral_angle_4_deg 13.125 r_dihedral_angle_1_deg 5.618 r_scangle_it 1.906 r_angle_refined_deg 1.314 r_scbond_it 1.191 r_mcangle_it 0.82 r_mcbond_it 0.467 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.094 r_dihedral_angle_3_deg 15.755 r_dihedral_angle_4_deg 13.125 r_dihedral_angle_1_deg 5.618 r_scangle_it 1.906 r_angle_refined_deg 1.314 r_scbond_it 1.191 r_mcangle_it 0.82 r_mcbond_it 0.467 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_symmetry_hbond_refined 0.009 r_gen_planes_refined 0.004 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 4421 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing