5JR2

Crystal structure of the EphA4 LBD in complex with APYd3 peptide inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4W4Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M MgCl2, 0.1 M Bis-Tris pH 6.5, 25% PEG 3,350, 3% 1,6-hexanediol

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.137	α = 90
b = 84.467	β = 93.87
c = 127.894	γ = 90

Symmetry
Space Group	P 1 21 1

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 HTC		2015-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.75	28.92	99.3	0.042	0.999	17.9	3.6		78825			17.1

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	1.75	1.78	96.5		0.316	3.1	3.1

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	4W4Z	1.75	28.92	74698	4103	99.21	0.17209	0.17036	0.20416	RANDOM	22.711

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]
-0.13		-0.07	-0.04		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.31
r_dihedral_angle_4_deg	14.852
r_dihedral_angle_3_deg	12.03
r_dihedral_angle_1_deg	6.63
r_long_range_B_refined	6.151
r_long_range_B_other	6.151
r_scangle_other	2.805
r_mcangle_it	2.21
r_mcangle_other	2.21
r_scbond_it	1.779
r_scbond_other	1.779
r_angle_refined_deg	1.591
r_angle_other_deg	1.322
r_mcbond_other	1.321
r_mcbond_it	1.32
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.007
r_gen_planes_other	0.006
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6077
Nucleic Acid Atoms
Solvent Atoms	685
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
Aimless	data scaling
PHASER	phasing
Coot	model building