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Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate at 1.45A resolution in space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NAL PDB ENTRY 1NAL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 100MM TRIS HCL, PH 8.2, 200MM AMMONIUM ACETATE, 18% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.329 α = 90 b = 108.049 β = 90 c = 148.309 γ = 90
Symmetry Space Group P 21 21 21
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 2007-12-12 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 1.45 63.42 96.2 0.08 11.6 5.1 213226 14.333
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 1.45 1.53 89.5 0.38 3.4 4.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NAL 1.45 87.33 202361 10718 95.86 0.16775 0.16665 0.18857 0.2884 RANDOM 15.594
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] -0.94 1.13 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.548 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_3_deg 12.148 r_dihedral_angle_1_deg 5.592 r_scangle_it 2.899 r_scbond_it 1.879 r_angle_refined_deg 1.346 r_angle_other_deg 1.268 r_mcangle_it 0.984 r_mcbond_it 0.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.548 r_dihedral_angle_4_deg 20.164 r_dihedral_angle_3_deg 12.148 r_dihedral_angle_1_deg 5.592 r_scangle_it 2.899 r_scbond_it 1.879 r_angle_refined_deg 1.346 r_angle_other_deg 1.268 r_mcangle_it 0.984 r_mcbond_it 0.592 r_mcbond_other 0.199 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d r_gen_planes_other 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 9188 Nucleic Acid Atoms Solvent Atoms 1307 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing