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Crystal structure of a novel N-acetylneuraminic acid lyase from Corynebacterium glutamicum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291.15 0.1 M Tris, 1.2 M Lithium chloride, 30% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.43 49.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.506 α = 90 b = 96.285 β = 92.33 c = 163.288 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 315r 2013-11-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97908, 0.96406, 0.97929 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 50 97.7 0.088 0.094 0.034 11.2 7.6 319011 15.43
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 96.2 0.634 0.68 0.247 0.855 7.5 31290
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 MAD FREE R-VALUE 1.601 34.268 1.34 318951 16084 97.59 0.1648 0.1633 0.1658 0.1937 0.1947 19.12
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 12.324 f_angle_d 0.997 f_chiral_restr 0.041 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18295 Nucleic Acid Atoms Solvent Atoms 2978 Heterogen Atoms 60
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling SOLVE phasing RESOLVE model building PHENIX refinement PDB_EXTRACT data extraction