1YPT | pdb_00001ypt

CRYSTAL STRUCTURE OF YERSINIA PROTEIN TYROSINE PHOSPHATASE AT 2.5 ANGSTROMS AND THE COMPLEX WITH TUNGSTATE

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				THE CATALYTIC DOMAIN (RESIDUES 163 - 468) OF YOP51 WAS CRYSTALLIZED AT 22 DEGREES CELSIUS, IN A SOLUTION OF 10 - 16% POLYETHYLENE GLYCOL, 5% 2-METHYL-2,4-PENTANEDIOL, 0.1% B-MERCAPTOETHANOL, AND 1MM IMIDAZOLE, PH 7.2. SOURCE ONLY THE CATALYTIC DOMAIN (RESIDUES 163 - 468) WAS EXPRESSED FOR THIS PARTICULAR EXPERIMENT. THE 235 CYS TO ARG MUTATION WAS UNINTENTIONAL AND MOST LIKELY THE RESULT OF USING PCR TO CONSTRUCT THE PLASMID (SEE REFERENCE REMARK 1).

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.53	α = 90
b = 71.53	β = 90
c = 107.48	γ = 120

Symmetry
Space Group	P 32

Data Collection

Refinement

Statistics
Diffraction ID	Structure Solution Method	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-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION		2.5	7	2	17095		84	0.168	0.168	0.222

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
x_dihedral_angle_d	24.81
x_angle_deg	2.93
x_improper_angle_d	1.25
x_bond_d	0.013
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4290
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing