2EZ9 | pdb_00002ez9

Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1POW	pdb entry 1POW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	280	ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.9	56.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.661	α = 90
b = 154.517	β = 90
c = 165.64	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	IMAGE PLATE	MAR scanner 345 mm plate		2005-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B		EMBL/DESY, HAMBURG	BW7B

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	1.6	19.62	83	0.089	12.14	4.6	165388	165340	2	3.7	12.9

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	1.6	1.62	0.759	75.9	0.343	2.4	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	pdb entry 1POW	1.6	19.62	2	165388	165339	3328	82.942	0.159	0.159	0.1583	0.16	0.1804	0.18	RANDOM	13.157

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]
1.141			-0.663		-0.477

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.842
r_dihedral_angle_4_deg	17.946
r_dihedral_angle_3_deg	12.261
r_dihedral_angle_1_deg	5.867
r_scangle_it	2.891
r_scbond_it	1.736
r_angle_refined_deg	1.318
r_mcangle_it	0.918
r_mcbond_it	0.47
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.842
r_dihedral_angle_4_deg	17.946
r_dihedral_angle_3_deg	12.261
r_dihedral_angle_1_deg	5.867
r_scangle_it	2.891
r_scbond_it	1.736
r_angle_refined_deg	1.318
r_mcangle_it	0.918
r_mcbond_it	0.47
r_nbtor_refined	0.303
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.192
r_symmetry_hbond_refined	0.102
r_xyhbond_nbd_refined	0.095
r_chiral_restr	0.082
r_metal_ion_refined	0.025
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9046
Nucleic Acid Atoms
Solvent Atoms	1030
Heterogen Atoms	178

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	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.