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Structure of wild type E. coli N-acetylneuraminic acid lyase 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 100MM TRIS-HCL PH 8.0, 200MM NACL, 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.38 48.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.795 α = 90 b = 142.167 β = 109.01 c = 84.18 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 2008-10-25 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 2.2 79.56 100 0.11 7.6 3.7 61635 2 34.7
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 2.32 100 0.47 2.7 3.7
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 2.2 71.09 58519 3083 99.75 0.21424 0.21126 0.27151 0.3074 RANDOM 27.076
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] 25.43 9.56 1.78 -27.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.087 r_dihedral_angle_4_deg 22.125 r_dihedral_angle_3_deg 17.416 r_dihedral_angle_1_deg 6.92 r_scangle_it 2.46 r_scbond_it 1.619 r_angle_refined_deg 1.462 r_mcangle_it 1.048 r_angle_other_deg 0.93 r_mcbond_it 0.599
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.087 r_dihedral_angle_4_deg 22.125 r_dihedral_angle_3_deg 17.416 r_dihedral_angle_1_deg 6.92 r_scangle_it 2.46 r_scbond_it 1.619 r_angle_refined_deg 1.462 r_mcangle_it 1.048 r_angle_other_deg 0.93 r_mcbond_it 0.599 r_mcbond_other 0.13 r_chiral_restr 0.077 r_bond_refined_d 0.013 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 9127 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing