3CZU | pdb_00003czu

Crystal structure of the human ephrin A2- ephrin A1 complex

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, 1SHW
experimental model	PDB	1SHW	PDB ENTRIES 3C8X, 1SHW

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.19	0.22533	0.23	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