3MJ2 | pdb_00003mj2

X-ray crystal structure of ITK complexed with inhibitor BMS-509744

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MIY	PDB entry 3MIY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	283	20% PEG3350, 0.2m ammonium acetate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283K

Crystal Properties
Matthews coefficient	Solvent content
2	38.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.082	α = 90
b = 39.246	β = 93.69
c = 50.86	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	CCD	ADSC QUANTUM 315			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.0	SSRL	BL7-1

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	1.9	37.7	91.8	0.07	13.5		19376	17785

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)
1	1.9	1.97	55.2		0.283	2.1		1336

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 3MIY	1.9	37.7	16876	909	93.24	0.20803	0.20565	0.2047	0.25189	0.2512	RANDOM	24.864

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]
1.59		0.08	-0.64		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.468
r_dihedral_angle_4_deg	18.721
r_dihedral_angle_3_deg	13.517
r_dihedral_angle_1_deg	5.281
r_scangle_it	1.783
r_scbond_it	1.111
r_angle_refined_deg	1.006
r_mcangle_it	0.89
r_mcbond_it	0.511
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.186
r_nbd_refined	0.184
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2074
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	43

Software

Software
Software Name	Purpose
ADSC	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling