3FL7

Crystal structure of the human ephrin A2 ectodomain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C8X	PDB entries 3C8X, 2E7H
experimental model	PDB	2E7H	PDB entries 3C8X, 2E7H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	290.9	3.0% PEG 4000, 0.1M Sodium acetate, 0.1 M Cacodylate pH 5.5, 0.5 M NDSB 256, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.358	α = 90
b = 89.992	β = 90
c = 136.476	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 300 mm CCD	Mirrors	2008-11-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.97948	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.5	41	99.7	0.07	22.43	4.1		25966		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.59	98.1		0.375	2.94	4	2510

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entries 3C8X, 2E7H	2.5	40.59	24331	1311	98.49	0.24873	0.246	0.29943	RANDOM	35.468

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]
-5.42			9.4		-3.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.705
r_dihedral_angle_4_deg	19.003
r_dihedral_angle_3_deg	17.374
r_dihedral_angle_1_deg	6.639
r_mcangle_it	1.259
r_angle_refined_deg	1.241
r_scangle_it	1.126
r_mcbond_it	0.725
r_scbond_it	0.709
r_chiral_restr	0.082
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3658
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	18

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling