Experiment: 1WVG

Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		model from MAD experiment performed on Se-Met substituted CDP-D-glucose 4,6-dehydratase from Salmonella typhi

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch method	4.2	298	sodium/potassium phosphate, homopipes, pH 4.2, batch method, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.9	α = 90
b = 93.9	β = 90
c = 152.8	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	130	CCD	SBC		2004-03-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.96411	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	50	94.3	0.055	37.1	5.2	68364	68364

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.86	85.7		0.248	3.1	2.5	6117

Refinement

Statistics
Diffraction ID	Structure Solution 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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	model from MAD experiment performed on Se-Met substituted CDP-D-glucose 4,6-dehydratase from Salmonella typhi	1.8	50	68364	68364	6904	94.3	0.203	0.203	0.201	0.2673	0.27	random

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]

RMS Deviations
Key	Refinement Restraint Deviation
t_dihedral_angle_d	17.9
t_angle_deg	2.25
t_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5649
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	106

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
TNT	refinement
HKL-2000	data reduction