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Crystal structure of metal-free NeuB, an N-acetylneuraminate synthase from Neisseria meningitidis in complex with malate
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 6.2 291 3% (v/v) MPD
1.75M Malic acid
10mM magnesium chloride
10mM N-acetylneuraminic acid
Crystal Properties Matthews coefficient Solvent content 2.23 44.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.07 α = 90 b = 76.2 β = 90 c = 77.55 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++ 2008-01-29 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) Rrim I (All) Rpim I (All) CC (Half) 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 1.85 77.62 98.5 0.098 0.104 0.035 0.998 2.53 3.9 29645 23.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 0.673 0.248 0.915 3.1 3.8
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 1.85 46.48 1.35 29641 1506 98.5 0.1904 0.1876 0.1888 0.2425 0.2433 24.7
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 28.947 f_angle_d 0.806 f_chiral_restr 0.0521 f_bond_d 0.007 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2681 Nucleic Acid Atoms Solvent Atoms 339 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement CrystalClear data reduction CrystalClear data scaling MOLREP phasing