2ZYB | pdb_00002zyb

Crystal structure of phenylimidazo pyrazin 2 bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LCK	PDB ENTRY 3LCK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.2M (NH4)2SO4, 0.1M Sodium cacodylate, 30% PEG8000, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.15	α = 90
b = 73.973	β = 90
c = 92.857	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	RIGAKU JUPITER 210		2003-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.0	SPring-8	BL32B2

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	2.55	28.51	98.5	0.101	0.12	11.8	3.3	9817	9965			26.7

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)
	2.55	2.69	96.6		0.211	0.248	5.9	3.4	1372

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3LCK	2.55	15	8763	968	98.3	0.18336	0.17145	0.17	0.29127	0.29	RANDOM	8.431

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]
0.04			0.48		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.147
r_dihedral_angle_4_deg	21.433
r_dihedral_angle_3_deg	19.395
r_dihedral_angle_1_deg	8.825
r_scangle_it	6.602
r_scbond_it	4.969
r_mcangle_it	3.324
r_mcbond_it	2.315
r_angle_refined_deg	1.662
r_symmetry_hbond_refined	0.549

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.147
r_dihedral_angle_4_deg	21.433
r_dihedral_angle_3_deg	19.395
r_dihedral_angle_1_deg	8.825
r_scangle_it	6.602
r_scbond_it	4.969
r_mcangle_it	3.324
r_mcbond_it	2.315
r_angle_refined_deg	1.662
r_symmetry_hbond_refined	0.549
r_nbtor_refined	0.335
r_symmetry_vdw_refined	0.302
r_nbd_refined	0.275
r_xyhbond_nbd_refined	0.229
r_chiral_restr	0.138
r_gen_planes_refined	0.028
r_bond_refined_d	0.02

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2209
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
MOSFLM	data reduction
SCALA	data scaling
AMoRE	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.