4AW5 | pdb_00004aw5

Complex of the EphB4 kinase domain with an oxindole inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		IN-HOUSE APO STRUCTURE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.42	48.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.657	α = 90
b = 53.978	β = 111.06
c = 63.242	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93.2	CCD	MARRESEARCH		2002-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 32-ID		APS	32-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.33	54	100	0.12	11.4	3.7		12716		-3

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	2.33	2.46	100		0.46	1.8	3.6

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	IN-HOUSE APO STRUCTURE	2.33	58.72	12054	642	99.93	0.19439	0.19015	0.2	0.27894	0.28	RANDOM	49.445

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]
4.05		3.63	-3.27		1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.898
r_scangle_it	3.498
r_scbond_it	1.994
r_angle_refined_deg	1.938
r_mcangle_it	1.694
r_angle_other_deg	1.452
r_mcbond_it	0.921
r_symmetry_vdw_other	0.272
r_nbd_other	0.241
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.207
r_symmetry_vdw_refined	0.119
r_symmetry_hbond_refined	0.113
r_nbtor_other	0.107
r_chiral_restr	0.099
r_bond_refined_d	0.019
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2049
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing