Experiment: 2XYU

Crystal structure of EphA4 kinase domain in complex with VUF 12058

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y6M	PDB ENTRY 2Y6M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		AMMONIUM SULFATE, BISTRIS PH 5.5, PEG 10K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.544	α = 90
b = 91.545	β = 90
c = 97.959	γ = 90

Symmetry
Space Group	P 21 21 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	MARMOSAIC 225 mm CCD	MIRROR	2010-08-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	2.12	43.19	99.5	0.14	8.5	3.6		17378		6	20.96

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	2.12	2.23	98.2		0.69	1.9	3.6

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2Y6M	2.117	43.187	16232	822	93.16	0.1916	0.1894	0.1991	0.2298

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]
-1.3133			-2.233		3.5463

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.211
f_angle_d	1.024
f_chiral_restr	0.068
f_bond_d	0.009
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2030
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	58

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing