2IJM | pdb_00002ijm

Crystal Structure of Focal Adhesion Kinase Domain with 2 molecules in the Asymmetric Unit Complexed with ADP and ATP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JBA	PDB ENTRY 1JBA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	278	30% (v/v) PEG-600, 10% glycerol, 0.1M HEPES pH 7.5, 0.05M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.432	α = 99.81
b = 51.645	β = 103.55
c = 66.544	γ = 90.69

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	CCD	ADSC QUANTUM 4	CURVED SI (111)	2003-01-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	1.0	ALS	5.0.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.187	34.3	95.1	0.045	0.056	16.3	4.8	29887	28426		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.187	2.27	70.9		0.327	0.283	4.1	4.5	2144

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 (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1JBA	2.187	34.3	26989	26989	1436	100	0.21051	0.2073	0.27149	RANDOM	34.932

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]
0.39	0.11	-0.44	0.21	-1.91	-1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.083
r_dihedral_angle_4_deg	19.341
r_dihedral_angle_3_deg	17.284
r_dihedral_angle_1_deg	6.175
r_scangle_it	2.618
r_scbond_it	1.63
r_angle_refined_deg	1.365
r_mcangle_it	1.224
r_mcbond_it	0.733
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.083
r_dihedral_angle_4_deg	19.341
r_dihedral_angle_3_deg	17.284
r_dihedral_angle_1_deg	6.175
r_scangle_it	2.618
r_scbond_it	1.63
r_angle_refined_deg	1.365
r_mcangle_it	1.224
r_mcbond_it	0.733
r_nbtor_refined	0.306
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.178
r_symmetry_hbond_refined	0.169
r_symmetry_vdw_refined	0.166
r_chiral_restr	0.092
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4203
Nucleic Acid Atoms
Solvent Atoms	184
Heterogen Atoms	58

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.