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X-ray crystal structure of N-acetylneuraminic acid lyase in complex with pyruvate, with the phenylalanine at position 190 replaced with the non-canonical amino acid dihydroxypropylcysteine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 3350 (18-28%), 200mM NaCl, 100mM Tric/HCl pH 7.0-8.5
Crystal Properties Matthews coefficient Solvent content 2.07 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.49 α = 90 b = 134.3 β = 108.1 c = 79.46 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 PIXEL DECTRIS PILATUS 6M-F Mirrors 2013-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 75.54 99.4 0.071 0.998 11.2 4.7 120355 18.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 95.7 0.425 0.811 3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ah7 1.7 75.53 114242 6056 99.33 0.17515 0.1737 0.20254 0.2262 RANDOM 23.156
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] 0.72 -0.34 -0.16 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.937 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 12.089 r_dihedral_angle_1_deg 5.895 r_long_range_B_refined 4.378 r_long_range_B_other 4.378 r_scangle_other 3.331 r_scbond_it 2.058 r_scbond_other 2.057 r_mcangle_it 1.963
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.937 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 12.089 r_dihedral_angle_1_deg 5.895 r_long_range_B_refined 4.378 r_long_range_B_other 4.378 r_scangle_other 3.331 r_scbond_it 2.058 r_scbond_other 2.057 r_mcangle_it 1.963 r_mcangle_other 1.963 r_angle_refined_deg 1.371 r_mcbond_it 1.288 r_mcbond_other 1.288 r_angle_other_deg 1.048 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9275 Nucleic Acid Atoms Solvent Atoms 414 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing