2A3K

Crystal Structure of the Human Protein Tyrosine Phosphatase, PTPN7 (HePTP, Hematopoietic Protein Tyrosine Phosphatase)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1M Tris-HCl, 2.0M ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.4	47.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.125	α = 90
b = 80.968	β = 90
c = 100.392	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 225 mm CCD		2005-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9207	SLS	X10SA

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	2.55	50	99.4	0.128			10833	10833

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	2.55	2.64	96.9		0.48

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JLN	2.55	42.68	10366	10366	522	99.23	0.22184	0.22184	0.21897	0.27466	RANDOM	29.008

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]
-4.02			0.15		3.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.519
r_dihedral_angle_4_deg	19.021
r_dihedral_angle_3_deg	17.276
r_dihedral_angle_1_deg	6.512
r_scangle_it	1.913
r_angle_refined_deg	1.27
r_scbond_it	1.207
r_mcangle_it	0.817
r_mcbond_it	0.457
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.519
r_dihedral_angle_4_deg	19.021
r_dihedral_angle_3_deg	17.276
r_dihedral_angle_1_deg	6.512
r_scangle_it	1.913
r_angle_refined_deg	1.27
r_scbond_it	1.207
r_mcangle_it	0.817
r_mcbond_it	0.457
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.238
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.163
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2134
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.