4FEE

High-resolution structure of pyruvate oxidase in complex with reaction intermediate 2-hydroxyethyl-thiamin diphosphate carbanion-enamine, crystal B

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EZT	PDB ENTRY 2EZT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	280	1.5 M ammonium sulfate, 200 mM phosphate, 0.1 mM thiamine diphosphate, 1 mM magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.07	α = 90
b = 154.46	β = 90
c = 165.82	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC QUANTUM 315r	toroidal focusing mirror	2010-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9000	ESRF	ID14-4

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	1.13	30	97.5	0.094	0.115	7.33	2.9	549376	549376		-3	11.026

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	1.13	1.16	93.9		0.504	2.2

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	PDB ENTRY 2EZT	1.13	20	549376	549376	11565	95.1	0.1225	0.1495	RANDOM	11.9874

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
s_angle_d	291
s_zero_chiral_vol	43
s_non_zero_chiral_vol	8
s_approx_iso_adps	0.101
s_anti_bump_dis_restr	0.081
s_from_restr_planes	0.034
s_similar_adp_cmpnt	0.029
s_bond_d	0.014
s_similar_dist
s_rigid_bond_adp_cmpnt

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9032
Nucleic Acid Atoms
Solvent Atoms	1671
Heterogen Atoms	236

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
PHENIX	phasing
SHELXL-97	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 R01GM157729.