Experiment: 2YD5

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

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		5.6		0.1 M SODIUM ACETATE TRIHYDRATE, 20% ISOPROPANOL, 20% (W/V) PEG 4000, 0.25 MM HEPARIN DP10, PH 5.6 .

Crystal Properties
Matthews coefficient	Solvent content
2.51	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.95	α = 90
b = 76.95	β = 90
c = 68.74	γ = 120

Symmetry
Space Group	P 32 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	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	2.2	48	99.7	0.09	19.1	10.7		12272		-3	33.23

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	2.2	2.26	98.2		0.83	3.6	10.6

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	2.2	38.475	11699	566	95.21	0.1973	0.1955	0.1934	0.2326	0.2282	39.13

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]
5.9418			5.9418		-10.1376

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.871
f_angle_d	0.827
f_chiral_restr	0.054
f_bond_d	0.004
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1510
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
SCALA	data scaling
PHASER	phasing