4XD1

X-ray structure of the N-formyltransferase QdtF from Providencia alcalifaciens, W305A mutant, in the presence of TDP-Qui3N and N5-THF


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82935-7% PEG 8000, 100 mM HEPPS, 200 mM NaCl, 200 mM KCl, 5 mM TDP, 5 mM N5-THF
Crystal Properties
Matthews coefficientSolvent content
2.448.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.279α = 90
b = 78.279β = 90
c = 151.105γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352014-08-27MSINGLE 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
11.550970.0690.06911.24.67358273582
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5490.50.3642.32.5

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 REPLACEMENTTHROUGHOUTPDB entry 4XCZ1.535.0369887369597.010.181240.179810.20828RANDOM18.299
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]
0.550.55-1.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.08
r_dihedral_angle_4_deg14.143
r_dihedral_angle_3_deg12.942
r_dihedral_angle_1_deg6.479
r_angle_refined_deg2.084
r_angle_other_deg0.932
r_chiral_restr0.126
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.08
r_dihedral_angle_4_deg14.143
r_dihedral_angle_3_deg12.942
r_dihedral_angle_1_deg6.479
r_angle_refined_deg2.084
r_angle_other_deg0.932
r_chiral_restr0.126
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.001
r_bond_other_d
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3227
Nucleic Acid Atoms
Solvent Atoms605
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing