6EB0 | pdb_00006eb0

STRUCTURE OF 4-HYDROXYPHENYLACETATE 3-MONOOXYGENASE (HPAB), OXYGENASE COMPONENT FROM ESCHERICHIA COLI

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	291	MICRO BATCH UNDER OIL AT 291K USING 2 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN SODIUM CONCENTRATE AND A PRECIPITANT COCKTAIL CONTAINING 0.08 M CACODYLATE BUFFER CONTAINING 0.16 M MAGNESIUM ACETATE TETRAHYDRATE, 16% POLYETHYLENE GLYCOL 8000, AND 20% V/V GLYCEROL, PH 6.0, MICROBATCH UNDER OIL

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.409	α = 90
b = 93.734	β = 108.23
c = 142.335	γ = 90

Symmetry
Space Group	C 1 2 1

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	MARMOSAIC 300 mm CCD	Rosenbaum Optics	2013-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.979	APS	22-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	2.37	46.363	99.3	0.113	15.81	4.3		90432

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	2.37	2.46	93.5		0.475	3.27	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2YYG	2.37	46.363	1.35	90403	4400	99.25	0.1615	0.1598	0.16	0.1954	0.2

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
f_dihedral_angle_d	10.933
f_angle_d	0.85
f_chiral_restr	0.053
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16396
Nucleic Acid Atoms
Solvent Atoms	833
Heterogen Atoms	12

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing
PHENIX	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.