5UIK

X-ray structure of the FdtF formyltransferase from salmonella enteric O60 in complex with TDP-Fuc3N and folinic acid


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 12-16% PEG 5000 200 mM NMe4Cl 10 mM folinic acid 10 mM TDP-Fuc3N
Crystal Properties
Matthews coefficientSolvent content
2.4850.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.237α = 90
b = 69.199β = 90
c = 200.641γ = 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
12.25097.20.0950.0957.94.146716
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)
12.22.391.30.3640.36422.3

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 REPLACEMENTTHROUGHOUT5UIJ2.248.0944292236697.270.209310.206040.27083RANDOM28.844
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]
1.23-0.08-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.919
r_dihedral_angle_4_deg18.848
r_dihedral_angle_3_deg16.903
r_dihedral_angle_1_deg6.772
r_long_range_B_refined5.27
r_long_range_B_other5.253
r_scangle_other3.705
r_mcangle_it2.958
r_mcangle_other2.958
r_scbond_it2.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.919
r_dihedral_angle_4_deg18.848
r_dihedral_angle_3_deg16.903
r_dihedral_angle_1_deg6.772
r_long_range_B_refined5.27
r_long_range_B_other5.253
r_scangle_other3.705
r_mcangle_it2.958
r_mcangle_other2.958
r_scbond_it2.256
r_scbond_other2.256
r_mcbond_it1.873
r_mcbond_other1.873
r_angle_refined_deg1.681
r_angle_other_deg0.972
r_chiral_restr0.091
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms294
Heterogen Atoms192

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing