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Structure of wild type E. coli N-acetylneuraminic acid lyase in complex with pyruvate in space group P21
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WKJ PDB ENTRY 2WKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 100 MM TRIS-HCL PH 8.2, 200 MM NACL, 18 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.693 α = 90 b = 142.456 β = 109.16 c = 83.626 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 2008-05-12 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 1.65 79.06 91.2 0.06 13.5 3.4 131694 2 19.85
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 1.65 1.74 60.8 0.32 3.2 2.9
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 2WKJ 1.65 79.07 125055 6596 90.56 0.21183 0.20986 0.2657 0.2492 0.3137 RANDOM 18.189
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] 20.22 4.67 -3.37 -16.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.871 r_dihedral_angle_4_deg 20.705 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 6.112 r_scangle_it 2.434 r_scbond_it 1.736 r_angle_refined_deg 1.404 r_mcangle_it 1.097 r_angle_other_deg 0.93 r_mcbond_it 0.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.871 r_dihedral_angle_4_deg 20.705 r_dihedral_angle_3_deg 13.992 r_dihedral_angle_1_deg 6.112 r_scangle_it 2.434 r_scbond_it 1.736 r_angle_refined_deg 1.404 r_mcangle_it 1.097 r_angle_other_deg 0.93 r_mcbond_it 0.683 r_mcbond_other 0.186 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 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 9120 Nucleic Acid Atoms Solvent Atoms 758 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing