2QT7 | pdb_00002qt7

Crystallographic structure of the mature ectodomain of the human receptor-type protein-tyrosine phosphatase IA-2 at 1.30 Angstroms

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	292	25% (w/v) PEG 4000, 0.1 M Tris pH 8.5, 0.2 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.756	α = 90
b = 66.799	β = 90
c = 73.131	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	ADSC QUANTUM 210	Toroidal focusing mirror	2006-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9793, 1.5895	NSLS	X6A

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	1.3	24	97.7	0.03	0.03	43.1	7.6	38269	38269			13.6

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)
	1.3	1.32	81.4		0.213	0.213	5.5	4.3	1587

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.3	23.97	38269	36265	1922	97.66	0.22159	0.22048	0.22	0.24216	0.24	RANDOM	15.782

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]
0.74					-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.001
r_dihedral_angle_4_deg	20.521
r_dihedral_angle_3_deg	11.001
r_dihedral_angle_1_deg	5.37
r_scangle_it	3.001
r_scbond_it	2.001
r_mcangle_it	1.479
r_angle_refined_deg	1.161
r_mcbond_it	0.884
r_nbtor_refined	0.301
r_nbd_refined	0.214
r_symmetry_vdw_refined	0.159
r_symmetry_hbond_refined	0.145
r_xyhbond_nbd_refined	0.131
r_metal_ion_refined	0.099
r_chiral_restr	0.08
r_symmetry_metal_ion_refined	0.04
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1383
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXDE	phasing