4KGD | pdb_00004kgd

High-resolution crystal structure of pyruvate oxidase from L. plantarum in complex with phosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FEE	PDB ENTRY 4FEE

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
2.87	57.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.28	α = 90
b = 154.16	β = 90
c = 165.47	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	2011-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.979200	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	1.06	35	94.9	0.07	0.081	9.68	3.38	645341	645341		-3	10.593

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	1.06	1.13	93.2		0.52	2.21

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R	PDB ENTRY 4FEE	1.06	30	625966	645341	19361	91.6	0.1271	0.1271	0.12	0.1505	0.14	RANDOM	12.8418

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
285	8946.42	11037.47

RMS Deviations
Key	Refinement Restraint Deviation
s_angle_d	310
s_zero_chiral_vol	79
s_non_zero_chiral_vol	6
s_approx_iso_adps	0.105
s_anti_bump_dis_restr	0.087
s_similar_adp_cmpnt	0.046
s_from_restr_planes	0.037
s_bond_d	0.015
s_similar_dist
s_rigid_bond_adp_cmpnt

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9048
Nucleic Acid Atoms
Solvent Atoms	1899
Heterogen Atoms	225

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHENIX	phasing
SHELXL	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.