4IM7

Crystal structure of fructuronate reductase (ydfI) from E. coli CFT073 (EFI TARGET EFI-506389) complexed with NADH and D-mannonate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	282	Protein solution was at 10 mg/mL containing 20 mM Tris (pH 7.5) and 100 mM NaCl. Mother liqueur contained 1.7 M ammonium sulfate, 0.085 M Hepes (pH 7.5), 1.7% PEG 400 and 15% glycerol, vapor diffusion, sitting drop, temperature 282K

Crystal Properties
Matthews coefficient	Solvent content
3	59.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.49	α = 90
b = 92.49	β = 90
c = 136	γ = 120

Symmetry
Space Group	P 31 2 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	RAYONIX MX-225		2012-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	30	99.9	0.09	11.42			53597		-3	27.297

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	99.9		0.611	2.55

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.9	29.551	2.02	53647	53593	2679	99.94	0.1496	0.1484	0.1728	random	23.6144

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]
-0.0825			-0.0825		0.165

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15
f_angle_d	1.105
f_chiral_restr	0.072
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3758
Nucleic Acid Atoms
Solvent Atoms	471
Heterogen Atoms	62

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.