5UIL

X-ray structure of the FdtF N-formyltransferase from Salmonella enterica O60 in complex with TDP-Fuc3N and tetrahydrofolate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5UIJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9293100 mM CHES 200 mM NMe4Cl 12-16% PEG 5000 10 mM TDP-Fuc3N 10 mM N-10-formyltetrahydrofolate
Crystal Properties
Matthews coefficientSolvent content
2.5852.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.671α = 90
b = 72.812β = 90
c = 191.738γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-05-18MSINGLE 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
12.25093.60.0990.0997.33.146550
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)
12.22.380.60.3210.3211.91.6

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 REPLACEMENTTHROUGHOUT5uij2.25044148236793.640.205770.202410.2701RANDOM26.089
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]
-0.582.05-1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.398
r_dihedral_angle_3_deg18.442
r_dihedral_angle_4_deg18.377
r_dihedral_angle_1_deg7.471
r_long_range_B_refined5.91
r_long_range_B_other5.891
r_scangle_other4.42
r_mcangle_it3.241
r_mcangle_other3.241
r_scbond_it2.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.398
r_dihedral_angle_3_deg18.442
r_dihedral_angle_4_deg18.377
r_dihedral_angle_1_deg7.471
r_long_range_B_refined5.91
r_long_range_B_other5.891
r_scangle_other4.42
r_mcangle_it3.241
r_mcangle_other3.241
r_scbond_it2.736
r_scbond_other2.736
r_mcbond_it2.073
r_mcbond_other2.073
r_angle_refined_deg1.725
r_angle_other_deg0.924
r_chiral_restr0.103
r_bond_refined_d0.012
r_gen_planes_refined0.006
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 Atoms6468
Nucleic Acid Atoms
Solvent Atoms316
Heterogen Atoms208

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing