3AYI | pdb_00003ayi

X-ray crystal structures of L-phenylalanine oxidase (deaminating and decaboxylating) from Pseudomonas sp. P501. Structures of the enzyme-ligand complex and catalytic mechanism

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YR4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	297	0.1M HEPES PH7.5, 1.0M AMMONIUM SULFATE, VAPOR DIFFUSION, pH 7.50, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.29	α = 90
b = 112.694	β = 90
c = 136.542	γ = 90

Symmetry
Space Group	P 21 21 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 210		2006-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A		Photon Factory	AR-NW12A

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	1.25	37.56	97.3	0.069		4.7		415716

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	1.25	1.32	87		0.329		4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	2YR4	1.25	37.56	394714	20896	97.1	0.105	0.104	0.12	0.131	0.14	RANDOM	11.8

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]
0.46			-0.04		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.924
r_dihedral_angle_4_deg	22.693
r_sphericity_free	22.337
r_dihedral_angle_3_deg	12.343
r_sphericity_bonded	7.51
r_scangle_it	6.718
r_dihedral_angle_1_deg	6.688
r_scbond_it	5.333
r_mcangle_it	3.588
r_mcbond_it	3.024
r_rigid_bond_restr	2.636
r_angle_refined_deg	2.442
r_angle_other_deg	1.202
r_mcbond_other	1.02
r_symmetry_hbond_refined	0.322
r_symmetry_vdw_other	0.273
r_nbd_refined	0.262
r_symmetry_vdw_refined	0.259
r_xyhbond_nbd_refined	0.247
r_nbd_other	0.229
r_nbtor_refined	0.194
r_chiral_restr	0.153
r_nbtor_other	0.097
r_xyhbond_nbd_other	0.09
r_bond_refined_d	0.03
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10424
Nucleic Acid Atoms
Solvent Atoms	2201
Heterogen Atoms	150

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling