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Structural Basis for Substrate Recognition in the Enzymatic Component of ADP-ribosyltransferase Toxin CDTa from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GIQ PDB ENTRY 1GIQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 0.1M MIB BUFFER PH 4.0, 20% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.091 α = 90 b = 42.744 β = 102.47 c = 77.004 γ = 90
Symmetry Space Group P 1 21 1
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 315 MIRRORS 2009-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 50 94 0.08 11.9 3.5 24824 31
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 2.07 75.3 0.32 1.94 1.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GIQ 2 25.06 22120 1201 93.95 0.22286 0.21976 0.27957 RANDOM 34.392
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] 0.02 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.608 r_dihedral_angle_4_deg 18.042 r_dihedral_angle_3_deg 14.699 r_dihedral_angle_1_deg 5.474 r_scangle_it 2.169 r_scbond_it 1.26 r_angle_refined_deg 1.079 r_mcangle_it 0.856 r_mcbond_it 0.447 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.608 r_dihedral_angle_4_deg 18.042 r_dihedral_angle_3_deg 14.699 r_dihedral_angle_1_deg 5.474 r_scangle_it 2.169 r_scbond_it 1.26 r_angle_refined_deg 1.079 r_mcangle_it 0.856 r_mcbond_it 0.447 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3137 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing