5UIM | pdb_00005uim

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UIJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	100 mM CHES 200 mM NMe4Cl 13-17% PEG 5000 10 mM folinic acid 10 mM TDP-Qui3N

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.31

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker Platinum 135	montel	2016-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	50	95.2	0.084	0.084	9.3	3.7		42547

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)	Redundancy	Number Unique Reflections (All)
1	2.2	2.3	86.6		0.295	0.295	1.9	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5uij	2.2	50	40390	2149	95.18	0.19799	0.19451	0.2	0.264	0.27	RANDOM	32.471

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		-1.11	2.01		-1.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.769
r_dihedral_angle_4_deg	22.765
r_dihedral_angle_3_deg	18.315
r_dihedral_angle_1_deg	7.511
r_long_range_B_refined	6.898
r_long_range_B_other	6.898
r_scangle_other	5.138
r_mcangle_other	4.033
r_mcangle_it	4.032
r_scbond_it	3.342
r_scbond_other	3.279
r_mcbond_it	2.673
r_mcbond_other	2.673
r_angle_refined_deg	1.699
r_angle_other_deg	0.902
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	6464
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	169

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing