7F5O

Crystal structure of PTPN2 catalytic domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L8K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.1 M Bis-Tris Propane (pH-7.5), 0.2 M Sodium Iodide, 20% w/v PEG 3350, 10% v/v Ethylene glycol and 0.9 mM Mitoxantrone additive

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.094	α = 111.54
b = 68.187	β = 102.659
c = 72.683	γ = 92.337

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	107	CCD	RAYONIX MX300HE		2019-10-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL15A1	1.0	NSRRC	BL15A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.7	25	96.4	0.022	0.98	33.7	2.5		100918

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.76	95.5		0.238	0.92	4.1	2.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1L8K	1.7	24.848	100506	4866	95.952	0.201	0.1989	0.241	19.305

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]
-0.062	0.131	0.056	-0.04	0.022	0.029

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.269
r_dihedral_angle_4_deg	20.315
r_dihedral_angle_3_deg	16.42
r_dihedral_angle_1_deg	6.752
r_lrange_it	5.512
r_lrange_other	5.421
r_scangle_it	3.824
r_scangle_other	3.819
r_mcangle_it	2.771
r_mcangle_other	2.771
r_scbond_it	2.416
r_scbond_other	2.41
r_mcbond_it	1.848
r_mcbond_other	1.845
r_angle_refined_deg	1.666
r_angle_other_deg	1.395
r_symmetry_xyhbond_nbd_other	0.379
r_symmetry_nbd_refined	0.247
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.211
r_nbd_other	0.192
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.17
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6955
Nucleic Acid Atoms
Solvent Atoms	553
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing