7N9G | pdb_00007n9g

Crystal structure of the Abl 1b Kinase domain in complex with Dasatinib and Imatinib

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	Ammonium dihydrogen phosphate

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.933	α = 90
b = 166.879	β = 90
c = 186.817	γ = 90

Symmetry
Space Group	I 2 2 2

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	RAYONIX MX300-HS		2018-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.2	46.7	99.9	0.083	0.03	0.999	15.1	8.6		55951		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	98.6		1.184	0.762		8.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2GQG	2.2	46.7	55936	2704	99.759	0.219	0.2174	0.22	0.2511	0.25	52.067

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]
3.585			-1.887		-1.698

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.255
r_dihedral_angle_3_deg	14.41
r_dihedral_angle_4_deg	11.506
r_lrange_it	7.474
r_lrange_other	7.473
r_dihedral_angle_1_deg	6.712
r_scangle_it	5.909
r_scangle_other	5.908
r_mcangle_it	4.741
r_mcangle_other	4.741
r_scbond_it	3.845
r_scbond_other	3.843
r_mcbond_it	3.17
r_mcbond_other	3.17
r_angle_refined_deg	1.289
r_angle_other_deg	1.244
r_nbd_refined	0.196
r_nbd_other	0.195
r_symmetry_nbd_other	0.176
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.145
r_xyhbond_nbd_refined	0.139
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.056
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5886
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	215

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing