3DKO | pdb_00003dko

Complex between the kinase domain of human ephrin type-a receptor 7 (epha7) and inhibitor alw-ii-49-7

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	WELL SOLUTION: 25% PEG 3350, 0.1 M NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS CRYOPROTECTED BY TRANSFER TO DROP CONTAINING MOTHER LIQUOR TO WHICH MPD WAS ADDED TO 25%, , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.658	α = 90
b = 52.658	β = 90
c = 217.059	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	RIGAKU RAXIS IV		2008-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

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	25	95.4	0.067	38.92	9.9	21903	21903		-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	2.07	98.1		0.417	4.19	6.5	2253

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 2REI	2	23.69	21809	20747	1062	95.3	0.19118	0.18917	0.19	0.2316	0.24	RANDOM	27.811

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]
1.06	0.53		1.06		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.222
r_dihedral_angle_4_deg	20.531
r_dihedral_angle_3_deg	12.401
r_dihedral_angle_1_deg	5.13
r_scangle_it	2.329
r_scbond_it	1.451
r_angle_refined_deg	1.156
r_mcangle_it	0.939
r_mcbond_it	0.599
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.222
r_dihedral_angle_4_deg	20.531
r_dihedral_angle_3_deg	12.401
r_dihedral_angle_1_deg	5.13
r_scangle_it	2.329
r_scbond_it	1.451
r_angle_refined_deg	1.156
r_mcangle_it	0.939
r_mcbond_it	0.599
r_nbtor_refined	0.3
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.155
r_xyhbond_nbd_refined	0.121
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2172
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	30

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.