3KKA | pdb_00003kka

Co-crystal structure of the sam domains of EPHA1 AND EPHA2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HIL	PDB ENTRY 3HIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293.1	2.1 M AMMONIUM SULPHATE, 2% PEG 400, 0.1 M NA HEPES PH 7.2.PRIOR TO SETTING UP CRYSTALLIZATION PLATES, CHYMOTRYPSIN WAS ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.57 MICROMOLAR., VAPOR DIFFUSION, HANGING DROP, temperature 293.1K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.554	α = 90
b = 56.071	β = 90
c = 107.617	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	ADSC QUANTUM 315		2009-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97932	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.4	33	100	0.106	20.16304	6.9	14362	14362		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.4	2.44	100		0.891	2.2083	6.4	704

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3HIL	2.4	30.44	13463	705	99.93	0.2015	0.19961	0.23	0.23463	0.25	RANDOM	54.789

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]
0.55			2.55		-3.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.759
r_dihedral_angle_4_deg	20.398
r_dihedral_angle_3_deg	20.25
r_dihedral_angle_1_deg	5.578
r_scangle_it	2.817
r_scbond_it	1.756
r_angle_refined_deg	1.392
r_mcangle_it	1.038
r_mcbond_it	0.561
r_chiral_restr	0.093

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.759
r_dihedral_angle_4_deg	20.398
r_dihedral_angle_3_deg	20.25
r_dihedral_angle_1_deg	5.578
r_scangle_it	2.817
r_scbond_it	1.756
r_angle_refined_deg	1.392
r_mcangle_it	1.038
r_mcbond_it	0.561
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2527
Nucleic Acid Atoms
Solvent Atoms	34
Heterogen Atoms	1

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.