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Native structure of N-acetylneuramininate lyase (sialic acid aldolase) from Aliivibrio salmonicida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F74 PDB ENTRY 1F74
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 25% PEG 1500, 20% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.942 α = 90 b = 86.28 β = 90 c = 117.733 γ = 90
Symmetry Space Group I 2 2 2
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 MARRESEARCH 2012-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 43.14 100 0.04 20.2 4.1 41377 2
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 1.74 100 0.58 2.8 4.1
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 1F74 1.65 43.18 39270 2081 99.92 0.16604 0.16423 0.1657 0.20122 0.2057 RANDOM 21.272
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] -0.74 2.56 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.797 r_dihedral_angle_4_deg 18.143 r_dihedral_angle_3_deg 12.784 r_dihedral_angle_1_deg 6.032 r_angle_refined_deg 2.196 r_chiral_restr 0.168 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.797 r_dihedral_angle_4_deg 18.143 r_dihedral_angle_3_deg 12.784 r_dihedral_angle_1_deg 6.032 r_angle_refined_deg 2.196 r_chiral_restr 0.168 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2263 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing