3N01 | pdb_00003n01

Crystal structure of an abridged form of the mature ectodomain of the Human Receptor-Type Protein Tyrosine Phosphatase ICA512/IA-2 at pH 8.5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QT7

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 calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.493	α = 90
b = 66.681	β = 90
c = 72.999	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 270	TOROIDAL FOCUSING MIRROR	2010-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9537	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	20	97.4	0.037	0.037	40.2	4.5	37730	37730

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	77.8		0.227	0.213	3	3.2	1469

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2QT7	1.3	20	37730	37648	1881	100	0.175	0.173	0.1661	0.213	0.2067	RANDOM	18.141

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]
0.14			-0.3		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.365
r_dihedral_angle_4_deg	17.756
r_dihedral_angle_3_deg	13.115
r_scangle_it	7.038
r_dihedral_angle_1_deg	6.379
r_scbond_it	4.995
r_mcangle_it	3.729
r_rigid_bond_restr	2.7
r_mcbond_it	2.571
r_angle_refined_deg	2.036
r_chiral_restr	0.142
r_bond_refined_d	0.031
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1288
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling