3C8X | pdb_00003c8x

Crystal structure of the ligand binding domain of human Ephrin A2 (Epha2) receptor protein kinase

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KGY	PDB entry 1KGY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	291.2	AN IN-SITU PROTEOLYSIS STRATEGY WAS USED TO GENERATE HIGH QUALITY CRYSTALS. TRYPSIN WAS ADDED FROM A 1.5 GRAM/L STOCK TO A PROTEIN SAMPLE (AT 6.2 GRAM/L) TO A FINAL TRYPSIN CONC OF 6.2 MICROGRAM/L BEFORE CRYSTAL PLATES WERE SET AT 291.2K. 25% PEG 3350, 0.1 M AMMONIUM SULFATE, 0.1 M BIS-TRIS PH 5.5. PARATONE-N WAS USED AS THE CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.518	α = 90
b = 92.518	β = 90
c = 41.291	γ = 120

Symmetry
Space Group	P 31 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 IV		2008-01-11	M	SINGLE WAVELENGTH

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

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	1.95	35	99.9	0.151	15.44	6.8	14975	14975		-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)
	1.95	2.02	98.6		0.849	1.8281	5	1453

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 1KGY	1.95	35	14205	755	99.8	0.16583	0.16291	0.17	0.22623	0.23	RANDOM	24.222

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]
1.44	0.72		1.44		-2.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.585
r_dihedral_angle_3_deg	14.527
r_dihedral_angle_4_deg	13.83
r_dihedral_angle_1_deg	7.161
r_scangle_it	4.785
r_scbond_it	3.616
r_mcangle_it	2.758
r_mcbond_it	1.953
r_angle_refined_deg	1.52
r_nbtor_refined	0.312

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1280
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	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.