3DZC

2.35 Angstrom resolution structure of WecB (VC0917), a UDP-N-acetylglucosamine 2-epimerase from Vibrio cholerae.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F6D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	1:1 V/V. Protein solution: 7.9mG/mL of protein, 0.5M NaCl, 10mM TRIS-HCL, 10 mM UDP. Reservoir solution (PACT, #23): 0.2M Calcium chloride, 0.1M MES, 20% w/v PEG 6000, pH 6.0, Vapor Diffusion, sitting drop, Temp. 295K., VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.391	α = 90
b = 88.127	β = 90
c = 132.193	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD	beryllium lenses	2008-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	2.35	30	100	0.095	17.9	6.6	40522	40522		-3	47.9

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	2.35	2.43	100		0.426	3.9	5.5	3962

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1F6D	2.35	30	38263	38263	2012	99.93	0.17542	0.17542	0.17238	0.17	0.23376	0.23	RANDOM	43.448

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]
-1.68			1.02		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.559
r_dihedral_angle_4_deg	11.303
r_dihedral_angle_3_deg	9.762
r_scangle_it	4.746
r_scbond_it	3.109
r_dihedral_angle_1_deg	2.351
r_mcangle_it	2.098
r_angle_refined_deg	1.612
r_mcbond_it	1.278
r_nbtor_refined	0.3

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5772
Nucleic Acid Atoms
Solvent Atoms	488
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.