6Y6I | pdb_00006y6i

lipopolysaccharide outer core galactosyltransferase WaaB and UDP complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y6G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1% tryptone, 1mM sodium azide, 0.05M HEPES pH7.0 and 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.44	α = 90
b = 104.44	β = 90
c = 89.64	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	81	CCD	ADSC QUANTUM 4		2015-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.979	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	73.85	99.9	0.16	1	16.1	23.4		38400

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.92	1.989	99.5		1.33	0.5		11.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	6Y6G	1.92	73.85	36421	1978	99.94	0.1662	0.1635	0.1661	0.2134	0.2126	RANDOM	33.397

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]
2.61			2.61		-5.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.227
r_dihedral_angle_4_deg	15.504
r_dihedral_angle_3_deg	13.928
r_dihedral_angle_1_deg	7.208
r_angle_refined_deg	1.375
r_angle_other_deg	1.352
r_rigid_bond_restr	0.965
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2849
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	25

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing