Experiment: 4AYL

Molecular structure of a metal-independent bacterial glycosyltransferase that catalyzes the synthesis of histo-blood group A antigen

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VS4	PDB ENTRY 2VS4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		15 % (W/V) PEG 4000, CONTAINING 0.1 M TRIS, PH 7.5, 0.2 M CALCIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.2	45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.227	α = 90
b = 41.227	β = 90
c = 282.944	γ = 90

Symmetry
Space Group	P 43 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	ADSC QUANTUM 315		2008-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.92	50	77.7	0.08	18.1	4.3		20120			21.7

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	1.92	1.99	22.2		0.1	4.5	1.6

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2VS4	1.919	35.368	1.37	15587	775	77.93	0.1811	0.1787	0.175	0.226	0.2223

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]
14.4947			14.4947		7.0638

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.268
f_angle_d	1.114
f_chiral_restr	0.076
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1754
Nucleic Acid Atoms
Solvent Atoms	200
Heterogen Atoms	17

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
MrBUMP	phasing
CHAINSAW	phasing