2WO2 | pdb_00002wo2

Crystal Structure of the EphA4-ephrinB2 complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KGY	PDB ENTRY 1KGY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6		30% PEG 6000, 1 M LITHIUM CHLORIDE, AND 100 MM MES PH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.371	α = 90
b = 107.371	β = 90
c = 47.619	γ = 120

Symmetry
Space Group	P 61

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	MAR scanner 345 mm plate	MIRRORS	2006-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.45	30	99.3	0.05	43.2	11.7		11645		-3	60.9

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	2.45	2.54	94.2		0.53	2.6	6.6

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 ENTRY 1KGY	2.45	28	11062	564	99.37	0.21784	0.21565	0.23	0.26021	0.27	RANDOM	49.394

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]
-0.9	-0.45		-0.9		1.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.651
r_dihedral_angle_3_deg	13.628
r_dihedral_angle_4_deg	13.187
r_dihedral_angle_1_deg	6.207
r_scangle_it	1.235
r_angle_refined_deg	1.064
r_angle_other_deg	0.727
r_scbond_it	0.704
r_mcangle_it	0.561
r_mcbond_it	0.295
r_chiral_restr	0.065
r_mcbond_other	0.036
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2533
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	14

Software

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