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Crystal structure of N-acetylneuraminic acid (Sialic acid) synthetase from Leptospira borgpetersenii serovar Hardjo-bovis in complex with citrate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 285 Molecular Dimensions Morpheus screen, condition G8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM each: sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate: 100mM MOPS/HEPES-Na pH 7.5: LpboA.19655.b.B1.PS38488 at 22.9mg/ml. For phasing, the crystal was incubated for 20sec in reservoir solution with additional 10% of 5M NaI in ethylene glycol (500mM final concentration). Cryo: direct: tray: 303852g8: puck hyz8-5.
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.88 α = 90 b = 49.12 β = 112.41 c = 88.85 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 RIGAKU SATURN 944+ RIGAKU VARIMAX 2017-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 43.375 97.1 0.057 0.06 0.999 25 10.241 50583 26.797
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 88.2 0.398 0.428 0.941 4.23 6.728
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.8 43.375 1.35 50574 2017 97.19 0.1573 0.1556 0.1561 0.1983 0.1974 0 24.9485
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 13.204 f_angle_d 0.824 f_chiral_restr 0.056 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4337 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 68
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing PARROT phasing ARP/wARP model building Coot model building