2Y9W

Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JS8	PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
experimental model	PDB	1LNL	PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
experimental model	PDB	1WX2	PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1
experimental model	PDB	1BT1	PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.6		10% PEG 4000, 100 MM NA ACETATE PH 4.6, 5 MM HOLMIUM CHLORIDE.

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.06	α = 90
b = 104.52	β = 90
c = 109.05	γ = 90

Symmetry
Space Group	P 21 21 2

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 315r		2008-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.3	61.1	100	0.12	7.7	3.7		53813			32.6

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	2.3	2.42	100		0.55	2.3	3.5

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	PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1	2.3	47.13	50366	2699	100	0.184	0.181	0.237	RANDOM	33.27

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]
-0.07			-0.01		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.451
r_dihedral_angle_3_deg	15.705
r_dihedral_angle_4_deg	13.663
r_dihedral_angle_1_deg	5.999
r_scangle_it	2.197
r_scbond_it	1.576
r_angle_refined_deg	1.164
r_mcangle_it	0.845
r_mcbond_it	0.437
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8518
Nucleic Acid Atoms
Solvent Atoms	389
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing