6Y6G | pdb_00006y6g

lipopolysaccharide outer core galactosyltransferase WaaB apo form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	297	1% tryptone, 1mM sodium azide, 0.05M HEPES pH7.0 and 20% w/v PEG 3350.

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.27	α = 90
b = 104.27	β = 90
c = 88.44	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 4r		2015-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.823	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	1.81	67.54	98.5	0.125	1	29	60.1		44277

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	1.81	1.875	86.2		0.863	0.6		18.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.81	67.54	42052	2225	98.45	0.1646	0.163	0.17	0.1956	0.2	RANDOM	30.493

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]
-1.11			-1.11		2.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.216
r_dihedral_angle_3_deg	13.08
r_dihedral_angle_4_deg	11.644
r_dihedral_angle_1_deg	6.707
r_angle_refined_deg	1.311
r_angle_other_deg	1.29
r_rigid_bond_restr	0.549
r_chiral_restr	0.081
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2837
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
pointless	data scaling
CRANK2	phasing