3I99

The crystal structure of the UDP-N-acetylenolpyruvoylglucosamine reductase from the Vibrio cholerae O1 biovar Tor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	289	0.1M Phosphate-citrate, 1.6M NaH2PO4/0.4M K2HPO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.334	α = 90
b = 84.334	β = 90
c = 53.335	γ = 90

Symmetry
Space Group	P 43

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	ADSC QUANTUM 315r	mirrors	2009-03-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794, 0.9796	APS	19-ID

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	2.2	99.33	99.33	0.138	18.48	6.9	18261	18139	2	2

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	2.2	2.257	96.82		0.75	2	5.2	1414

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.2	45.08	18139	984	99.33	0.17087	0.16794	0.22334	RANDOM	27.477

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]
-0.12			-0.12		0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.472
r_dihedral_angle_3_deg	17.802
r_dihedral_angle_4_deg	14.571
r_dihedral_angle_1_deg	7.052
r_scangle_it	5.279
r_scbond_it	3.313
r_angle_refined_deg	2.041
r_mcangle_it	1.961
r_mcbond_it	1.038
r_chiral_restr	0.152

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.472
r_dihedral_angle_3_deg	17.802
r_dihedral_angle_4_deg	14.571
r_dihedral_angle_1_deg	7.052
r_scangle_it	5.279
r_scbond_it	3.313
r_angle_refined_deg	2.041
r_mcangle_it	1.961
r_mcbond_it	1.038
r_chiral_restr	0.152
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2626
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement

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 R01GM133198.