1PH0 | pdb_00001ph0

Non-carboxylic Acid-Containing Inhibitor of PTP1B Targeting the Second Phosphotyrosine Site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PTY	PDB entry 1PTY and internal refinement of other PTP1B:ligand complexes

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.1	277	Precipiation buffer: 100 mM Hepes, 0.2 M Magnesium Acetate, 14% v/v PEG8000, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.94	α = 90
b = 88.94	β = 90
c = 105.363	γ = 120

Symmetry
Space Group	P 31 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	MARRESEARCH	mirrors	2001-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	20	96.3	0.08	0.08	20.9	4.41	24002	22263		1	32.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	75.4		0.375	0.375	2.1	4.1	1852

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1PTY and internal refinement of other PTP1B:ligand complexes	2.2	19.8	2	22229	19340	1932	77.5	0.213	0.192	0.227	RANDOM	35.1

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]
2.3	6.49		2.3		-4.61

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.3
c_scangle_it	5.92
c_scbond_it	3.95
c_mcangle_it	3.93
c_mcbond_it	2.48
c_angle_deg	1.3
c_improper_angle_d	0.73
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2301
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	46

Software

Software
Software Name	Purpose
CNX	refinement
MAR345	data collection
HKL-2000	data scaling
CNX	phasing