2IVV

Crystal structure of phosphorylated RET tyrosine kinase domain complexed with the inhibitor PP1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		IN-HOUSE PART-REFINED STRUCTURE OF RET KINASE DOMAIN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	PROTEIN 1.5 MG/ML IN 20 MM TRIS-HCL PH 8.0, 100MM NACL, 1MM DTT, 1MM EDTA, 1MM SODIUM VANADATE RESERVOIR 2.8 M SODIUM FORMATE, 0.1 M SODIUM CITRATE PH 4.5, 0.2M LITHIUM CHLORIDE VAPOUR DIFFUSION, SITTING DROP, 289 K

Crystal Properties
Matthews coefficient	Solvent content
2.74	57.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.641	α = 90
b = 70.955	β = 101.79
c = 78.685	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	IMAGE PLATE	MARRESEARCH	MIRROR	2006-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.25	26.1	99.8	0.06	10.6	3.9		18394

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.37	99.8		0.2	3.9	3.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	IN-HOUSE PART-REFINED STRUCTURE OF RET KINASE DOMAIN	2.25	25.67	17476	916	99.9	0.187	0.185	0.237	RANDOM	38.65

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]
0.34		0.82	0.11		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.118
r_dihedral_angle_4_deg	17.974
r_dihedral_angle_3_deg	13.789
r_dihedral_angle_1_deg	5.689
r_scangle_it	3.716
r_scbond_it	2.496
r_mcangle_it	1.63
r_angle_refined_deg	1.535
r_mcbond_it	0.96
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.212
r_nbd_refined	0.203
r_xyhbond_nbd_refined	0.179
r_symmetry_hbond_refined	0.165
r_chiral_restr	0.103
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2158
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing