5UIN

X-ray structure of the W305A variant of the FdtF N-formyltransferase from salmonella enteric O60


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293100 mM MOPS 13-16% PEG 3350 200 mL LiCl 5 mM TDP 5 mM folinic acid
Crystal Properties
Matthews coefficientSolvent content
2.4950.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.467α = 90
b = 59.457β = 96.25
c = 107.599γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 135montel2016-06-29MSINGLE 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
12.25098.70.0950.0959.14.145968
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)
12.22.396.60.2640.2642.82.4

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 REPLACEMENTTHROUGHOUT5uij2.25043635232198.70.190780.187540.25221RANDOM21.474
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]
-0.66-0.192.25-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.173
r_dihedral_angle_3_deg18.271
r_dihedral_angle_4_deg17.913
r_dihedral_angle_1_deg7.245
r_long_range_B_refined5.429
r_long_range_B_other5.429
r_scangle_other4.024
r_scbond_other2.565
r_scbond_it2.553
r_mcangle_other2.455
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.173
r_dihedral_angle_3_deg18.271
r_dihedral_angle_4_deg17.913
r_dihedral_angle_1_deg7.245
r_long_range_B_refined5.429
r_long_range_B_other5.429
r_scangle_other4.024
r_scbond_other2.565
r_scbond_it2.553
r_mcangle_other2.455
r_mcangle_it2.453
r_angle_refined_deg1.874
r_mcbond_other1.606
r_mcbond_it1.605
r_angle_other_deg0.987
r_chiral_restr0.107
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms6454
Nucleic Acid Atoms
Solvent Atoms374
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing