The crystal structure of Escherichia coli TdcF, a member of the highly conserved YjgF/YER057c/UK114 family

BMC Structural Biology

Table 2 Summary of X-ray data and model parameters for TdcF

Data set	As-isolated (ethylene glycol)	As-isolated (PEG 400)	2-Ketobutyrate soak	Propionate soak
Data collection
Radiation source	RU-H3RHB	1D14-2 ESRF	1D14-2 ESRF	RU-H3RHB
Wavelength (Å)	1.542	0.933	0.933	1.542
Cell parameters (Å)	a = 72.7 b = 86.2 c = 62.6	a = 72.7 b = 86.4 c = 62.6	a = 72.6 b = 85.9 c = 62.7	a = 72.4 b = 85.7 c = 62.5
Resolution range^a (Å)	23.7 – 2.35 (2.43 – 2.35)	35.9 – 1.60 (1.63 – 1.60)	35.4 -1.60 (1.63 – 1.60)	25.5 – 2.45 (2.54 – 2.45)
Unique reflections	16863	50526	49876	14841
Completeness^a (%)	99.3 (95.2)	95.2 (66.4)	94.9 (71.2)	98.9 (94.0)
Redundancy	4.4	2.9	3.3	3.4
R_merge ^a,b	0.103 (0.368)	0.071 (0.116)	0.060 (0.243)	0.077 (0.303)
<I/σ (I)>^a	12.1 (2.7)	19.1 (3.8)	20.5 (2.1)	14.6 (3.2)
Wilson B value (Å²)	29.5	15.8	17.1	35.9
Refinement
R_cryst ^c (based on 95% of data; %)	17.2	15.5	16.2	16.6
R_free ^c (based on 5% of data; %)	24.4	19.9	20.4	25.3
DPI^d (based on R_free; Å)	0.257	0.087	0.089	0.295
Ramachandran plot^e (%)	94.0	95.8	95.5	94.6
Rmsd bond distances (Å)	0.020	0.017	0.015	0.021
Rmsd bond angles (°)	1.800	1.555	1.441	1.843
Contents of model
Protein (residues/atoms)	383/2876	381/2886	381/2895	382/2860
Waters (molecules)	205	457	400	195
Ligands (molecules/atoms)	2/8	1/7	3/21	2/10
Ligands (identity^f/sites occupied)	EDO/B,C	SER/C	2KT/A,B,C	PPI/B,C
Average temperature factors (Å ² )
Main-chain atoms	17.7	13.0	14.9	21.0
Side-chain atoms	18.5	15.6	17.4	21.6
Waters	23.1	29.8	30.8	26.8
Ligands	29.4	19.2	24.7	33.8
Overall	18.4	16.4	17.9	27.7
PDB accession code	2UYJ	2UYK	2UYN	2UYP

^a The figures in brackets indicate the values for outer resolution shell.
^b R_merge = Σ_hΣ_l|I_hl- <I_h>|/Σ_hΣ_l<I_h>, where I_lis the l^th observation of reflection h and <I_h> is the weighted average intensity for all observations l of reflection h.
^c The R-factors R_cryst and R_free are calculated as follows: R = Σ (|F_obs - F_calc|)/Σ |F_obs| × 100, where F_obs and F_calc are the observed and calculated structure factor amplitudes, respectively.
^d Diffraction-component precision index [32] – an estimate of the overall coordinate errors calculated in REFMAC5 [29].
^e Residues with most favoured Φ/Ψ angles as calculated using PROCHECK [33].
^f EDO = ethylene glycol (1,2-ethanediol); 2KT = 2-ketobutyrate; PPI = propionate.

ISSN: 1472-6807