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Crystal structure of tRNA dependent lantibiotic dehydratase MibB from Microbispora sp. 107891
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 100 mM HEPES pH 7.5, 20-24% ethanol;
100 mM MOPS pH 7.9, 20-24% ethanol
Crystal Properties Matthews coefficient Solvent content 2.71 54.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.137 α = 90 b = 151.112 β = 90 c = 205.744 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 210 2013-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 0.987 CHESS A1
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 2.7 50 99 0.065 26.6 5.9 72174
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 2.7 2.75 99.8 0.772 2 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MIR FREE R-VALUE 2.708 45.239 1.35 70209 3537 96.12 0.2068 0.2038 0.2068 0.2644 0.2652
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.622 f_angle_d 1.36 f_chiral_restr 0.082 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16088 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Coot model building SHARP phasing HKL-2000 data scaling HKL-2000 data collection HKL-2000 data reduction