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Structure of the E192N mutant of E. coli N-acetylneuraminic acid lyase in space group P21
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 8.2 100 MM TRIS-HCL PH 8.2, 200 MM NACL, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.63 α = 90 b = 142.77 β = 108.99 c = 84.487 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 2009-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.8 47.59 98.4 0.09 8.3 3.6 110985 2 26.78
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 1.8 1.9 97.2 0.39 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2WNN 1.8 39.95 105488 5446 97.54 0.19928 0.1966 0.25312 0.3 RANDOM 22.724
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] 11.89 7.32 -1.42 -10.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.57 r_dihedral_angle_4_deg 20.803 r_dihedral_angle_3_deg 15.082 r_dihedral_angle_1_deg 6.279 r_scangle_it 2.126 r_scbond_it 1.452 r_angle_refined_deg 1.327 r_mcangle_it 0.98 r_angle_other_deg 0.927 r_mcbond_it 0.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.57 r_dihedral_angle_4_deg 20.803 r_dihedral_angle_3_deg 15.082 r_dihedral_angle_1_deg 6.279 r_scangle_it 2.126 r_scbond_it 1.452 r_angle_refined_deg 1.327 r_mcangle_it 0.98 r_angle_other_deg 0.927 r_mcbond_it 0.581 r_mcbond_other 0.144 r_chiral_restr 0.075 r_bond_refined_d 0.011 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 9170 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing