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Structure of the Y137A mutant of E. coli N-acetylneuraminic acid lyase in complex with pyruvate, N-acetyl-D-mannosamine and N- acetylneuraminic acid
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, 200MM NACL, 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.97 α = 90 b = 143.22 β = 109.51 c = 83.41 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 2009-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 49.5 98.7 0.09 9.6 3.6 82202 2 21.4
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 2.11 95.7 0.41 2.8 3.5
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 49.46 78080 4084 98.07 0.18247 0.17964 0.1846 0.2349 0.2269 RANDOM 27.7
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] 50.39 -7.26 -24.13 -26.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.238 r_dihedral_angle_4_deg 18.903 r_dihedral_angle_3_deg 15.342 r_dihedral_angle_1_deg 6.439 r_scangle_it 2.059 r_scbond_it 1.383 r_angle_refined_deg 1.342 r_angle_other_deg 0.901 r_mcangle_it 0.863 r_mcbond_it 0.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.238 r_dihedral_angle_4_deg 18.903 r_dihedral_angle_3_deg 15.342 r_dihedral_angle_1_deg 6.439 r_scangle_it 2.059 r_scbond_it 1.383 r_angle_refined_deg 1.342 r_angle_other_deg 0.901 r_mcangle_it 0.863 r_mcbond_it 0.506 r_mcbond_other 0.117 r_chiral_restr 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 9166 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing