3F4A

Structure of Ygr203w, a yeast protein tyrosine phosphatase of the Rhodanese family

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	0.1 M Tris 8,5, 1.5 M LiSO4 plus 0.015 mg/ml trypsin. Cryoprotected with N-paratone oil, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.382	α = 90
b = 72.025	β = 103.6
c = 53.514	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	ADSC QUANTUM 315	Mirrors	2008-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	APS	19-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	1.75	50	98.7	0.08	25.682	3.6	27702	27354			19.6

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)
	1.75	1.81	89.3		0.295	2.6	2.6

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	SAD	THROUGHOUT	none	1.8	36.01	24128	1281	99.7	0.16808	0.16575	0.21064	RANDOM	21.415

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]
0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.046
r_dihedral_angle_3_deg	15.365
r_dihedral_angle_4_deg	14.072
r_dihedral_angle_1_deg	5.372
r_scangle_it	3.899
r_scbond_it	2.863
r_angle_refined_deg	1.564
r_mcangle_it	1.539
r_mcbond_it	1.236
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.279
r_symmetry_hbond_refined	0.236
r_nbd_refined	0.211
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.115
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2462
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	42

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling