Experiment: 4AYJ

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	4AYL	PDB ENTRY 4AYL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	BOGT6A (4 MG/ML) AND SACCHARIDE (10 MM) WERE INCUBATED OVERNIGHT AT 16 DEG C AND CRYSTALS WERE GROWN IN A WELL SOLUTION CONTAINING 20 % PEG 3350, 0.1 M BIS-TRIS PROPANE, PH 8.5 AND 0.2 M NA/K TARTRATE

Crystal Properties
Matthews coefficient	Solvent content
2.16	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.85	α = 90
b = 93.87	β = 93.82
c = 75.51	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2009-03-07	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	3	70.7	94.1	0.13	9.3	3.9		18669			47.78

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	3	3.16	93.7		0.5	2.6	3.8

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 4AYL	3	70.693	1.36	18641	950	93.65	0.185	0.1807	0.7089	0.2619	0.7072

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]
15.7734		19.9858	-1.9054		11.7961

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.58
f_angle_d	1.429
f_chiral_restr	0.104
f_bond_d	0.009
f_plane_restr	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7807
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	132

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing