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Clostridium difficile Toxin A C-terminal fragment 1 (TcdA-f1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 295 250 mM ammonium tartrate, 100 mM sodium acetate, 20% glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.05 α = 90 b = 42.05 β = 90 c = 132.11 γ = 90
Symmetry Space Group P 41 21 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 CCD ADSC QUANTUM 4 2004-09-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.979571,0.979741,1.019867 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 40.16 99.3 0.057 0.057 21.4 6.4 10716 10716 -3 -3 15
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 95.7 0.187 0.187 7.4 6.2 1015
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 1.85 40.16 10199 10199 516 99.04 0.16191 0.16191 0.15979 0.1627 0.205 0.2119 RANDOM 13.84
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] 0.1 0.1 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.328 r_scangle_it 5.745 r_scbond_it 3.93 r_mcangle_it 2.929 r_mcbond_it 1.96 r_angle_refined_deg 0.996 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.328 r_scangle_it 5.745 r_scbond_it 3.93 r_mcangle_it 2.929 r_mcbond_it 1.96 r_angle_refined_deg 0.996 r_nbd_refined 0.185 r_symmetry_vdw_refined 0.174 r_xyhbond_nbd_refined 0.127 r_symmetry_hbond_refined 0.121 r_chiral_restr 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 988 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing