3LU1 | pdb_00003lu1

Crystal Structure Analysis of WbgU: a UDP-GalNAc 4-epimerase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SB8	PDB ENTRY 1SB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Microbatch under oil	10	298	Ammonium Sulfate, PEG 3350, Glycine, pH 10, Microbatch under oil, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.13	α = 90
b = 78.13	β = 90
c = 231.924	γ = 120

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	103.15	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL1-5	1.5	SSRL	BL1-5

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.5	44.028	94.7	0.13	0.13	13.5	4.3	51939	51939

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.56	88.8		0.882	0.882	0.8	4.1	3563

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	PDB ENTRY 1SB8	2.5	44.028	51878	2637	94.72	0.207	0.204	0.2035	0.258	0.2581	RANDOM	36.806

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]
0.72	0.36		0.72		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.669
r_dihedral_angle_3_deg	17.634
r_dihedral_angle_4_deg	14.22
r_dihedral_angle_1_deg	5.228
r_scangle_it	1.473
r_angle_refined_deg	1.149
r_scbond_it	0.847
r_mcangle_it	0.647
r_mcbond_it	0.339
r_chiral_restr	0.081
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10684
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	368

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction