4MZU

Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthermodel from SAD experiment

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM HEPPS, 7-12% PEG-8000, 100 mM MgCl2, 10 mM dTDP, 10 mM CoA, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7655.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.314α = 79.23
b = 109.443β = 79.98
c = 127.847γ = 84.89
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2012-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9794APS19-BM

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
12.23091.10.0710.071273205722205772
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.28870.2230.2234.72.519668

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTmodel from SAD experiment2.2302057721954881028490.880.207510.207510.204210.26985RANDOM35.626
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]
0.451.160.58-2.130.571.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.011
r_dihedral_angle_4_deg23.834
r_dihedral_angle_3_deg19.948
r_dihedral_angle_1_deg7.804
r_scangle_it5.063
r_scbond_it3.287
r_angle_refined_deg2.23
r_mcangle_it2.051
r_mcbond_it1.133
r_chiral_restr0.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.011
r_dihedral_angle_4_deg23.834
r_dihedral_angle_3_deg19.948
r_dihedral_angle_1_deg7.804
r_scangle_it5.063
r_scbond_it3.287
r_angle_refined_deg2.23
r_mcangle_it2.051
r_mcbond_it1.133
r_chiral_restr0.153
r_bond_refined_d0.013
r_gen_planes_refined0.01
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_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 AtomsNumber
Protein Atoms26574
Nucleic Acid Atoms
Solvent Atoms847
Heterogen Atoms962

Software

Software
Software NamePurpose
HKL-3000data collection
SOLVEphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling