5UIM

X-ray structure of the FdtF N-formyltransferase from salmonella enteric O60 in complex with folinic acid and TDP-Qui3N


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 13-17% PEG 5000 10 mM folinic acid 10 mM TDP-Qui3N
Crystal Properties
Matthews coefficientSolvent content
2.3848.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.236α = 90
b = 58.406β = 96.04
c = 106.781γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-06-06MSINGLE 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
12.25095.20.0840.0849.33.742547
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)
12.22.386.60.2950.2951.91.7

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 REPLACEMENTTHROUGHOUT5uij2.25040390214995.180.197990.194510.264RANDOM32.471
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]
-0.19-1.112.01-1.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.769
r_dihedral_angle_4_deg22.765
r_dihedral_angle_3_deg18.315
r_dihedral_angle_1_deg7.511
r_long_range_B_refined6.898
r_long_range_B_other6.898
r_scangle_other5.138
r_mcangle_other4.033
r_mcangle_it4.032
r_scbond_it3.342
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.769
r_dihedral_angle_4_deg22.765
r_dihedral_angle_3_deg18.315
r_dihedral_angle_1_deg7.511
r_long_range_B_refined6.898
r_long_range_B_other6.898
r_scangle_other5.138
r_mcangle_other4.033
r_mcangle_it4.032
r_scbond_it3.342
r_scbond_other3.279
r_mcbond_it2.673
r_mcbond_other2.673
r_angle_refined_deg1.699
r_angle_other_deg0.902
r_chiral_restr0.097
r_bond_refined_d0.013
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 Atoms6464
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms169

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing