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Structure of the C. difficile TcdB cysteine protease domain in complex with a peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HO6 PDB entry 3HO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 0.1M Tris HCl pH 8.0, 30% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.31 α = 90 b = 45.48 β = 103.53 c = 87.23 γ = 90
Symmetry Space Group C 1 2 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 315r 2009-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
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 50 100 0.116 9.2 6.7 33449 28.2
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 2.11 100 0.534 2.9 5.8 4808
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 3HO6 2 50 31754 1692 99.99 0.18759 0.18504 0.1859 0.23282 0.2318 RANDOM 35.055
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] -0.22 0.6 1.47 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.589 r_dihedral_angle_4_deg 15.314 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 5.523 r_scangle_it 2.719 r_scbond_it 1.667 r_angle_refined_deg 1.304 r_mcangle_it 1.076 r_mcbond_it 0.56 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.589 r_dihedral_angle_4_deg 15.314 r_dihedral_angle_3_deg 13.978 r_dihedral_angle_1_deg 5.523 r_scangle_it 2.719 r_scbond_it 1.667 r_angle_refined_deg 1.304 r_mcangle_it 1.076 r_mcbond_it 0.56 r_chiral_restr 0.076 r_bond_refined_d 0.01 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3886 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 119
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling