5K8C

X-ray structure of KdnB, 3-deoxy-alpha-D-manno-octulosonate 8-oxidase, from Shewanella oneidensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RF7PDB entry 3RF7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52777-9% PEG-8000, 100 mM homopipes, 1 M tetramethylammonium chloride
Crystal Properties
Matthews coefficientSolvent content
3.1661.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.594α = 90
b = 107.594β = 90
c = 149.861γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.8593.1899.30.0830.08311.27.644036
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.95990.3993.14.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3RF71.8593.1841818221899.340.180520.178510.21811RANDOM19.154
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]
0.480.240.48-1.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.577
r_dihedral_angle_4_deg21.318
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg6.559
r_long_range_B_refined6.248
r_long_range_B_other6.247
r_scangle_other4.258
r_scbond_it2.871
r_scbond_other2.865
r_mcangle_other2.423
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.577
r_dihedral_angle_4_deg21.318
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg6.559
r_long_range_B_refined6.248
r_long_range_B_other6.247
r_scangle_other4.258
r_scbond_it2.871
r_scbond_other2.865
r_mcangle_other2.423
r_mcangle_it2.422
r_angle_refined_deg2.042
r_mcbond_it1.729
r_mcbond_other1.728
r_angle_other_deg1.085
r_chiral_restr0.123
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2774
Nucleic Acid Atoms
Solvent Atoms438
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing