Experiment: 2X11

Crystal structure of the complete EphA2 ectodomain in complex with ephrin A5 receptor binding domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CZU	PDB ENTRIES 3CZU, 3FL7, 1SHW
experimental model	PDB	3FL7	PDB ENTRIES 3CZU, 3FL7, 1SHW
experimental model	PDB	1SHW	PDB ENTRIES 3CZU, 3FL7, 1SHW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				TWO PARTS OF PROTEIN SOLUTION WERE MIXED WITH ONE PART WATER, ONE PART RESERVOIR SOLUTION (8 % POLYETHYLENE GLYCOL 6000, 0.8 M LICL, 0.08 M CITRATE PH 5) AND ONE PART 1 % POLYVINYLPYRROLIDONE K15.

Crystal Properties
Matthews coefficient	Solvent content
3.61	66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.63	α = 90
b = 59.63	β = 90
c = 112.16	γ = 90

Symmetry
Space Group	P 2 2 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 4		2008-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	4.8	173	98.2	0.11	12.95	6.2		6016		1	166.11

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	4.8	4.9	75.7		0.74	2.8	6.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 ENTRIES 3CZU, 3FL7, 1SHW	4.83	40.482	0.03	5643	260	93.69	0.313	0.3123	0.3044	0.3143	0.3078

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]
-46.5561			-4.8023		48.1254

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.707
f_angle_d	0.675
f_chiral_restr	0.044
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4870
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing