5UIJ

X-ray structure of The FdtF N-formyltransferase from Salmonella enteric O60 in complex with TDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XCZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MOPS 15-18% PEG 3350 5 mM TDP
Crystal Properties
Matthews coefficientSolvent content
2.5451.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.91α = 90
b = 64.757β = 90.54
c = 97.757γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-05-05MSINGLE 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
11.997.7595.60.0630.06312.63.770013
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)
11.9287.20.2780.2782.51.8

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 REPLACEMENTTHROUGHOUT4xcz1.997.7566447355295.560.183320.180810.23126RANDOM26.351
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]
-0.240.521.44-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.195
r_dihedral_angle_4_deg18.077
r_dihedral_angle_3_deg17.043
r_dihedral_angle_1_deg7.203
r_long_range_B_refined7.099
r_long_range_B_other7.099
r_scangle_other5.848
r_scbond_it4.058
r_scbond_other4.058
r_mcangle_it3.465
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.195
r_dihedral_angle_4_deg18.077
r_dihedral_angle_3_deg17.043
r_dihedral_angle_1_deg7.203
r_long_range_B_refined7.099
r_long_range_B_other7.099
r_scangle_other5.848
r_scbond_it4.058
r_scbond_other4.058
r_mcangle_it3.465
r_mcangle_other3.465
r_mcbond_it2.679
r_mcbond_other2.679
r_angle_refined_deg1.995
r_angle_other_deg0.944
r_chiral_restr0.124
r_bond_refined_d0.011
r_gen_planes_refined0.008
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 Atoms6463
Nucleic Acid Atoms
Solvent Atoms555
Heterogen Atoms109

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing