3OP0 | pdb_00003op0

Crystal structure of Cbl-c (Cbl-3) TKB domain in complex with EGFR pY1069 peptide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FBV	PDB ID: 1FBV CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277.15	20% Jeffamine M-600, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.25	α = 90
b = 90.25	β = 90
c = 191.581	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	CCD	ADSC Q315 3X3 CCD	KIRKPATRICK BAEZ BIMORPH MIRROR PAIR	2010-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.52	49.45	100	0.13	9.1	5.7		29742			49

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)
	2.52	2.66	100		0.745	2	5.6

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 (All)	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 ID: 1FBV CHAIN A	2.52	49.45	29663	28157	1505	99.7	0.255	0.216	0.214	0.21	0.266	0.26	RANDOM	35.9

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]
2.68	1.34		2.68		-4.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.33
r_dihedral_angle_4_deg	18.52
r_dihedral_angle_3_deg	16.615
r_dihedral_angle_1_deg	14.708
r_scangle_it	1.573
r_angle_refined_deg	1.543
r_angle_other_deg	1.17
r_scbond_it	1.162
r_mcangle_it	0.546
r_mcbond_it	0.32
r_mcbond_other	0.1
r_chiral_restr	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5163
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	4

Software

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