Experiment: 7KJB

Crystal structure of the EphA2 S897E/S901E mutant intracellular KD-SAM domains

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PDO	4PDO, 3KKA
experimental model	PDB	3KKA	4PDO, 3KKA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	287	4.5% Tacsimate, 0.09 M HEPES pH 7.0, 9% PEG-MME 5K, 0.1 M CsCl

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.456	α = 90
b = 94.456	β = 90
c = 99.646	γ = 120

Symmetry
Space Group	P 32 2 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		2016-04-07	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)	Rrim I (All)	Rpim I (All)	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	2.8	29.53	99.9	0.285	0.313	0.13	0.992	10.2	10.9		13051			50.49

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	100		1.956	2.153	0.895	0.554	1.4	11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4PDO, 3KKA	2.8	29.53	1.34	13025	665	99.98	0.2	0.1976	0.1985	0.246	0.24	57.16

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.7367
f_angle_d	0.4993
f_chiral_restr	0.0407
f_bond_d	0.0027
f_plane_restr	0.0027

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2882
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	1

Software

Software
Software Name	Purpose
CrystalClear	data collection
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement