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Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate and the inhibitor (2R,3R)-2,3,4- trihydroxy-N,N-dipropylbutanamide in space group P21 crystal form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WNN PDB ENTRY 2WNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 100MM TRIS-HCL PH 8.2, 200 MM NACL, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.02 α = 90 b = 143.741 β = 109.9 c = 84.304 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 ADSC CCD 2008-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 79.31 98.6 0.09 8.6 3.5 78597 2 24.528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 96.3 0.44 2.6 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WNN 2.05 71.88 74586 3966 97.68 0.19176 0.18951 0.1912 0.23394 0.2345 RANDOM 22.926
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] 36.75 5.88 -8.33 -28.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.261 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 13.218 r_dihedral_angle_1_deg 5.609 r_scangle_it 2.571 r_scbond_it 1.602 r_angle_refined_deg 1.283 r_mcangle_it 1.048 r_angle_other_deg 0.904 r_mcbond_it 0.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.261 r_dihedral_angle_4_deg 17.827 r_dihedral_angle_3_deg 13.218 r_dihedral_angle_1_deg 5.609 r_scangle_it 2.571 r_scbond_it 1.602 r_angle_refined_deg 1.283 r_mcangle_it 1.048 r_angle_other_deg 0.904 r_mcbond_it 0.583 r_mcbond_other 0.122 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9192 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing