☰ Navigation Tabs
Activator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostridium difficile without nucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4EHT PDB ENTRY 4EHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 23 mg/mL protein in 50 mM MOPS, pH 7.2, 120 mM sodium chloride, 1.4 mM ADP, 9 mM magnesium chloride, 1 mM D-desthiobiotin, 6 mM DTT, 1.4 mM sodium dithionite, 100 mM sodium fluoride, 10 mM aluminum trifluoride, reservoir: 8% w/v PEG8000, 25% v/v MPD, 0.35 M sodium chloride, pH 8.5 (drop: 1 uL + 1 uL), VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.02 59.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.136 α = 90 b = 113.136 β = 90 c = 56.032 γ = 90
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 RAYONIX MX-225 2008-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3 30 99.4 0.059 21.32 7.3 7197 7197 2 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.1 99.7 0.486 4.35 7.6
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4EHT 3 19.672 1.99 7197 7195 360 99.76 0.1751 0.1717 0.1742 0.2356 0.2434
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] -8.1371 -8.1371 16.2743
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.116 f_angle_d 1.138 f_chiral_restr 0.065 f_bond_d 0.009 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1936 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 4
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing PHENIX refinement XDS data reduction XDS data scaling