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The X-ray structure of L-threonine dehydrogenase from the common hospital pathogen Clostridium difficile.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 5 microlitres of enzyme at a concentration of 5 mg/ml and 5 microlitres of 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5, 30 % v/v PEG 4000 (Molecular Dimensions Limited Structure Screen I, condition 35).
Crystal Properties Matthews coefficient Solvent content 5.8 78.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.87 α = 90 b = 180.87 β = 90 c = 88.35 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 2M 2012-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.56 63.28 99.5 0.118 0.118 0.125 0.04 0.998 12.2 9.3 53475
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.56 2.7 99.4 1.778 1.778 1.897 0.646 0.526 0.4 8.3
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 FREE R-VALUE 5lc1 2.6 63.28 47443 2500 97.28 0.2024 0.2004 0.2072 0.2389 0.24 RANDOM 75.367
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] -2.95 -1.47 -2.95 9.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_4_deg 23.026 r_dihedral_angle_3_deg 20.797 r_dihedral_angle_1_deg 8.637 r_angle_refined_deg 1.79 r_angle_other_deg 1.297 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.911 r_dihedral_angle_4_deg 23.026 r_dihedral_angle_3_deg 20.797 r_dihedral_angle_1_deg 8.637 r_angle_refined_deg 1.79 r_angle_other_deg 1.297 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5030 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction