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X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FRK PDB entry 3FRK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 295 16-21% PEG-3350, 100 mM MES, 200 mM KCl, 150 mM MgCl2, 1 mM PLP, 50 mM monosodium glutamate
Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 266.628 α = 90 b = 61.675 β = 102.03 c = 99.636 γ = 90
Symmetry Space Group C 1 2 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 Bruker Platinum 135 2015-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.15 50 95.8 0.078 0.078 7.8 2.9 83041
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 2.15 2.25 89.4 0.254 2.4 1.8
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 3FRK 2.15 50 78941 4100 95.82 0.1742 0.17144 0.1795 0.22571 0.2291 RANDOM 22.988
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] -1.31 -0.81 2.69 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_4_deg 20.801 r_dihedral_angle_3_deg 16.805 r_dihedral_angle_1_deg 6.95 r_long_range_B_refined 5.305 r_long_range_B_other 5.263 r_scangle_other 4.107 r_mcangle_it 3.057 r_mcangle_other 3.057 r_scbond_it 2.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.498 r_dihedral_angle_4_deg 20.801 r_dihedral_angle_3_deg 16.805 r_dihedral_angle_1_deg 6.95 r_long_range_B_refined 5.305 r_long_range_B_other 5.263 r_scangle_other 4.107 r_mcangle_it 3.057 r_mcangle_other 3.057 r_scbond_it 2.639 r_scbond_other 2.639 r_angle_refined_deg 2.126 r_mcbond_it 2.01 r_mcbond_other 2.01 r_angle_other_deg 1.183 r_chiral_restr 0.147 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12192 Nucleic Acid Atoms Solvent Atoms 710 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing