2YD2

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Sigma

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2YD4	PDB ENTRY 2YD4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.2		0.2M AMMONIUM IODIDE, 20% W/V PEG 3350, PH 6.2 .

Crystal Properties
Matthews coefficient	Solvent content
2.38	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.4	α = 90
b = 29.49	β = 92.61
c = 61.58	γ = 90

Symmetry
Space Group	C 1 2 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	ASDC QUANTUM 4R			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	29	98.1	0.08	13.7	3.5		7438		-3	24.6

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	2.6	84.8		0.67	2.6	3.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2YD4	2.552	27.237	6759	322	89.24	0.1995	0.1962	0.19	0.2602	0.26	31.8

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]
-7.183		-4.5739	-3.4048		-6.4729

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.321
f_angle_d	0.905
f_chiral_restr	0.061
f_bond_d	0.006
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1524
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	7

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
SCALA	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.