Experiment: 4XT0

Crystal Structure of Beta-etherase LigF from Sphingobium sp. strain SYK-6

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	1 uL protein solution (10mM HEPES pH 7.5, 50mM NaCl, 0.5mM TCEP, 1mM glutathione) mixed with 0.8 uL of the well solution (25% MEPEG 2000, 0.2M TMAO, 0.1M BTP pH 9) and 0.2 uL of a suspension of LigF micro-crystals (0.2M Magnesium formate, 30% PEG 3350, 1mM glutathione) Cryoprotected with 30% MEPEG 2000, 0.2M TMAO, 0.1M Tris pH 8.5, 1mM glutathione

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.708	α = 90
b = 123.708	β = 90
c = 66.416	γ = 120

Symmetry
Space Group	P 63 2 2

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	MARMOSAIC 300 mm CCD		2014-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

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	2.07	40.493	99.8	0.076	0.079	0.019	11.9	17.3		18884			24.29

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	2.07	2.11	98.3		0.637	0.663	0.181	0.922		12.9	899

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.07	40.493	1.35	18232	963	96.42	0.161	0.1581	0.159	0.2143	0.214	40.8004

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	14.593
f_angle_d	1.022
f_chiral_restr	0.042
f_bond_d	0.008
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1975
Nucleic Acid Atoms
Solvent Atoms	262
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
Coot	model building