5N7E | pdb_00005n7e

Crystal structure of the Dbl-homology domain of Bcr-Abl in complex with monobody Mb(Bcr-DH_4).

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JE4	Chain A: homology model based on 4JE4, Chain B: homology model based on 2Z0Q
experimental model	PDB	2Z0Q	Chain A: homology model based on 4JE4, Chain B: homology model based on 2Z0Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.12 M monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M buffer system 2 pH 7.5 (Sodium HEPES; MOPS (acid)); 50% precipitant mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.122	α = 90
b = 55.568	β = 105.46
c = 45.031	γ = 90

Symmetry
Space Group	C 1 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	PIXEL	DECTRIS PILATUS 2M-F		2015-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999870	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.647	43.402	99.27	0.03673	0.02165	0.999	18.29	3.8		47055

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.647	1.706	93.25		0.5916	0.3474	0.946			4391

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	Chain A: homology model based on 4JE4, Chain B: homology model based on 2Z0Q	1.647	43.402	1.35	47055	2451	99.27	0.1852	0.1833	0.19	0.2194	0.22	36.1086

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.145
f_angle_d	0.808
f_chiral_restr	0.054
f_bond_d	0.006
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2200
Nucleic Acid Atoms
Solvent Atoms	348
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing

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.