2YR6

Crystal structure of L-phenylalanine oxidase from Psuedomonas sp.P501

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	293	0.1M HEPES pH7.5, 1.0M ammonium sulfate, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.877	α = 90
b = 113.029	β = 90
c = 136.463	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		2005-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.00000	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	1.35	34.18	99.9	0.089		5.5		339311

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	1.35	1.42	100		0.342		5.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2YR4	1.35	34.18	322071	17132	99.82	0.10439	0.10263	0.13769	RANDOM	12.85

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]
0.75			-0.35		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.62
r_sphericity_free	24.119
r_dihedral_angle_4_deg	21.295
r_dihedral_angle_3_deg	11.858
r_sphericity_bonded	8.167
r_scangle_it	7.15
r_dihedral_angle_1_deg	6.744
r_scbond_it	5.765
r_mcangle_it	3.911
r_mcbond_it	3.339
r_rigid_bond_restr	2.928
r_angle_refined_deg	2.475
r_angle_other_deg	1.27
r_mcbond_other	1.153
r_symmetry_hbond_refined	0.318
r_nbd_refined	0.251
r_symmetry_vdw_other	0.251
r_xyhbond_nbd_refined	0.238
r_nbd_other	0.225
r_symmetry_vdw_refined	0.202
r_nbtor_refined	0.193
r_chiral_restr	0.174
r_nbtor_other	0.097
r_xyhbond_nbd_other	0.046
r_bond_refined_d	0.031
r_gen_planes_refined	0.015
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10424
Nucleic Acid Atoms
Solvent Atoms	1957
Heterogen Atoms	148

Software

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