3CZU

Crystal structure of the human ephrin A2- ephrin A1 complex

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.6	290.9	14.9% PEG 4000, 0.1M Sodium citrate pH 5.6, 20% Isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K, pH 5.60

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.431	α = 90
b = 99.431	β = 90
c = 204.879	γ = 120

Symmetry
Space Group	P 65 2 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	IMAGE PLATE	RIGAKU RAXIS IV		2008-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT

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	2.65	25	100	0.109	35.74	20.8		18122		-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	2.65	2.74	100		0.714	5.509	21.2

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, 1SHW	2.65	24.86	17120	938	99.94	0.19507	0.19343	0.22533	RANDOM	42.445

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]
0.19	0.09		0.19		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.89
r_dihedral_angle_3_deg	16.557
r_dihedral_angle_4_deg	15.66
r_dihedral_angle_1_deg	6.59
r_scangle_it	3.59
r_scbond_it	2.206
r_mcangle_it	1.703
r_angle_refined_deg	1.225
r_mcbond_it	1.006
r_nbtor_refined	0.313
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.102
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2473
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	39

Software

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