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X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RF7 PDB entry 3RF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 7-9% PEG-8000, 100 mM homopipes, 1 M tetramethylammonium chloride
Crystal Properties Matthews coefficient Solvent content 3.16 61.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.594 α = 90 b = 107.594 β = 90 c = 149.861 γ = 120
Symmetry Space Group P 63 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 Bruker Platinum 135 2015-06-15 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 1.85 93.18 99.3 0.083 0.083 11.2 7.6 44036
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 1.85 1.95 99 0.399 3.1 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3RF7 1.85 93.18 41818 2218 99.34 0.18052 0.17851 0.1873 0.21811 0.224 RANDOM 19.154
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] 0.48 0.24 0.48 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.577 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 6.559 r_long_range_B_refined 6.248 r_long_range_B_other 6.247 r_scangle_other 4.258 r_scbond_it 2.871 r_scbond_other 2.865 r_mcangle_other 2.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.577 r_dihedral_angle_4_deg 21.318 r_dihedral_angle_3_deg 14.761 r_dihedral_angle_1_deg 6.559 r_long_range_B_refined 6.248 r_long_range_B_other 6.247 r_scangle_other 4.258 r_scbond_it 2.871 r_scbond_other 2.865 r_mcangle_other 2.423 r_mcangle_it 2.422 r_angle_refined_deg 2.042 r_mcbond_it 1.729 r_mcbond_other 1.728 r_angle_other_deg 1.085 r_chiral_restr 0.123 r_bond_refined_d 0.011 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2774 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing