2PA5

Crystal structure of human protein tyrosine phosphatase PTPN9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2HNQ	PDB entry 2HNQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.15	293	25% PEG 3350, 0.2 M Potassium thiocyanate, 10% Ethylene glycol, 0.1 M Bis-Tris propane pH 6.15, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.965	α = 77.44
b = 57.427	β = 78.22
c = 66.446	γ = 80.41

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	100	CCD	MARMOSAIC 225 mm CCD		2007-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.95370	SLS	X10SA

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	1.6	33.96	96.9	0.063	0.063	9	2	71616	71616			13.9

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)
1	1.6	1.69	95.3		0.379	0.379	2.1	1.9	19981

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 2HNQ	1.6	33.96	68013	68013	3602	96.94	0.15726	0.15726	0.15559	0.18792	RANDOM	11.67

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]
0.19	-0.14		0.07	0.13	-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.278
r_dihedral_angle_4_deg	14.843
r_dihedral_angle_3_deg	11.354
r_scangle_it	8.173
r_scbond_it	5.985
r_dihedral_angle_1_deg	5.578
r_mcangle_it	4.264
r_mcbond_it	3.055
r_mcbond_other	1.898
r_angle_refined_deg	1.434
r_angle_other_deg	1.153
r_symmetry_vdw_other	0.239
r_nbd_refined	0.225
r_nbd_other	0.2
r_nbtor_refined	0.184
r_symmetry_vdw_refined	0.169
r_symmetry_hbond_refined	0.158
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.09
r_nbtor_other	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4637
Nucleic Acid Atoms
Solvent Atoms	405
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing