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Crystal Structure of a putative D-Mannonate oxidoreductase from Haemophilus influenza (Avi_5165, TARGET EFI-513796) with bound NAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Protein (16.36 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 5% Glycerol, 10 mM NAD); Reservoir (0.2 M Lithium Chloride, 20 %(w/v) PEG 3350
); Cryoprotection (80% Reservoir + 20% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.976 α = 90 b = 138.382 β = 90 c = 115.942 γ = 90
Symmetry Space Group C 2 2 21
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 MX225HE MIRRORS 2014-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 1.55 100 99.7 0.098 9.3 8.2 79010 13.43
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 1.55 1.58 100 0.893 8 3933
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 SAD FREE R-VALUE 1.551 23.084 1.34 74635 3688 94.22 0.1422 0.1407 0.1431 0.1716 0.1708 21.6162
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 13.927 f_angle_d 1.29 f_chiral_restr 0.049 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4270 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 180
Software Software Software Name Purpose PHENIX refinement Aimless data scaling HKL-2000 data scaling PDB_EXTRACT data extraction PHENIX phasing