2EZ8 | pdb_00002ez8

Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-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	hanging drop	5.7	280	ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.9	56.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.133	α = 90
b = 154.462	β = 90
c = 165.656	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	1.97	24.96	98.2	0.107	11.49	4.5	105614	105590	2	3.7	12.8

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	1.97	2	0.871	87.1	0.275	3.5	3.7

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	1.963	24.96	2	105614	105590	2105	97.964	0.149	0.149	0.1486	0.15	0.1722	0.17	RANDOM	13.078

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]
1.953			-1.008		-0.945

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.135
r_dihedral_angle_4_deg	19.193
r_dihedral_angle_3_deg	13.47
r_dihedral_angle_1_deg	6.155
r_scangle_it	3.715
r_scbond_it	2.22
r_angle_refined_deg	1.463
r_mcangle_it	1.153
r_mcbond_it	0.611
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.135
r_dihedral_angle_4_deg	19.193
r_dihedral_angle_3_deg	13.47
r_dihedral_angle_1_deg	6.155
r_scangle_it	3.715
r_scbond_it	2.22
r_angle_refined_deg	1.463
r_mcangle_it	1.153
r_mcbond_it	0.611
r_nbtor_refined	0.301
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.191
r_symmetry_hbond_refined	0.137
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9046
Nucleic Acid Atoms
Solvent Atoms	993
Heterogen Atoms	186

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.