7EED

Crystal structure of EphA7 mutant D751H

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295.15	PEG3350, Ammonium sulphate, HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.24	α = 90
b = 51.24	β = 90
c = 215.271	γ = 120

Symmetry
Space Group	P 65

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		2021-01-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54184

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	3.05	71.76	92.5	0.185	0.988	11.2	1		5689

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.05	3.22			0.988

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2REI	3.05	44.375	5376	255	92.524	0.201	0.1994	0.247	27.178

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]
0.526	0.263		0.526		-1.705

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.784
r_dihedral_angle_4_deg	20.486
r_dihedral_angle_3_deg	18.363
r_dihedral_angle_1_deg	8.584
r_lrange_it	2.266
r_lrange_other	2.265
r_angle_refined_deg	1.68
r_angle_other_deg	1.199
r_mcangle_it	0.691
r_mcangle_other	0.69
r_mcbond_it	0.358
r_mcbond_other	0.358
r_symmetry_xyhbond_nbd_refined	0.273
r_scangle_it	0.252
r_scangle_other	0.252
r_nbd_refined	0.23
r_nbd_other	0.209
r_symmetry_nbd_other	0.201
r_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.168
r_symmetry_nbd_refined	0.134
r_symmetry_nbtor_other	0.079
r_scbond_it	0.071
r_scbond_other	0.071
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2212
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing