6IL9 | pdb_00006il9

One Glycerol complexed Crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ILB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8.5	287	0.2 M MgCl2, 15% (w/v) PEG 3350, and 0.1 M Tris (base)/HCl (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 147.148	α = 90
b = 52.35	β = 103.405
c = 73.997	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS3 6M		2017-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	0.98000	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.72	50	99.9	0.105	0.114	0.043	8.2	6.8		58374			22.0750964293

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.72	1.75	99.5		0.469	0.508	0.194	0.918		6.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	6ILB	1.72005356106	35.7847621218	1.40353220837	58290	2979	99.6716938545	0.183340469848	0.181511831401	0.18	0.217545035719	0.22	RANDOM	25.6107222967

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	7.07578781259
f_angle_d	0.776304485016
f_chiral_restr	0.0519684894388
f_bond_d	0.00585893381229
f_plane_restr	0.00460866270686

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3900
Nucleic Acid Atoms
Solvent Atoms	474
Heterogen Atoms	7

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
SCALEPACK	data scaling
HKL-2000	data collection
HKL-2000	data reduction
MOLREP	phasing

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.