7EEC | pdb_00007eec

Crystal structure of EphA7 mutant G656R

X-RAY DIFFRACTION

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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
2.42	49.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.78	α = 90
b = 51.78	β = 90
c = 216.08	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		2020-11-11	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	3.1	72.03	100	0.175	0.984	11.9	1		5944

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	3.1	3.27			0.175

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2REI	3.1	44.8428	5944	294	100	0.183	0.1813	0.18	0.2101	0.22	32.018

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]
0.056	0.028		0.056		-0.182

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.463
r_dihedral_angle_3_deg	16.956
r_dihedral_angle_4_deg	15.355
r_dihedral_angle_1_deg	7.887
r_angle_refined_deg	1.589
r_angle_other_deg	1.209
r_lrange_it	0.901
r_lrange_other	0.901
r_symmetry_xyhbond_nbd_refined	0.322
r_nbd_refined	0.225
r_nbd_other	0.219
r_symmetry_nbd_other	0.2
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.169
r_symmetry_nbd_refined	0.162
r_mcangle_it	0.157
r_mcangle_other	0.157
r_symmetry_xyhbond_nbd_other	0.09
r_mcbond_it	0.081
r_mcbond_other	0.081
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.062
r_scangle_it	0.054
r_scangle_other	0.054
r_xyhbond_nbd_other	0.015
r_scbond_it	0.012
r_scbond_other	0.012
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2211
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms

Software

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