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Crystal structure N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate bound halide free active site)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8U8W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Morpheus C11: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaNO3, 30 mM Na2HPO4 and 30 mM (NH4)2SO4 KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Cryo: direct. This structure has no halides near KPI 165 in the active which resulted in movement of a nearby loop is the previous structures.
Crystal Properties Matthews coefficient Solvent content 4.09 69.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.4 α = 90 b = 96.4 β = 90 c = 205.596 γ = 120
Symmetry Space Group P 62 2 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 PIXEL Bruker PHOTON III 2023-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 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 2.1 46.93 100 0.229 0.232 0.036 0.999 17.9 42.6 33838
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 2.1 2.16 100 1.93 1.963 0.354 0.789 30.7
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.1 46.93 1.34 33767 1649 99.97 0.1843 0.1827 0.1877 0.2142 0.2167
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 15.254 f_angle_d 0.894 f_chiral_restr 0.047 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2283 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing