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Crystal structure of N-acetylneuraminate lyase (NanA) from Klebsiella aerogenes (pyruvate and halides bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 Morpheus B11: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Tris/BICINE, pH 8.5, 30 mM NaF, 30 mM NaBr and 30 mM NaI. KlaeA.01563.a.B1.PW39186 at 18.6 mg/mL. 2mM pyruvate added to the protein prior to crystallization. Plate 13191 well B11 drop 2. Puck: PSL-1309, Cryo: direct
Crystal Properties Matthews coefficient Solvent content 4.18 70.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.413 α = 90 b = 97.413 β = 90 c = 205.512 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 DECTRIS EIGER2 XE 9M 2023-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9795 NSLS-II 19-ID
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 1.8 48.71 100 0.085 0.086 0.014 0.999 28.5 39.4 54224
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 1.8 1.84 99.9 2.605 2.639 0.417 0.942 39.5
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 1.8 32.6 1.35 53979 2643 99.68 0.1647 0.1636 0.171 0.1868 0.1849
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 14.15 f_angle_d 0.995 f_chiral_restr 0.053 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2287 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 34
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing