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Crystal structure of NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis, in complex with manganese, inorganic phosphate, and N-acetylmannosamine (NeuB.Mn2+.Pi.ManNAc)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 1.75 M malic acid, pH 6.2
2M NaH2PO4, pH 6.2,
10 mM MnCl2,
10 mM ManNAc,
10 mM NeuNAc oxime,
10 mM NH2OH
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.99 α = 90 b = 75.86 β = 90 c = 77.66 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2007-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 2.4 46.46 99.2 0.109 9.1 3.93 13862 28.56
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 2.4 2.48 98.5 0.344 4 3.86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 1XUZ 2.4 29.69 1.37 13859 706 99.23 0.183 0.1787 0.1797 0.2652 0.2669 30.93
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 15.0101 f_angle_d 0.865 f_chiral_restr 0.0514 f_bond_d 0.0076 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2667 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing