2X2M

Crystal Structure of phosphorylated RET tyrosine kinase domain with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IVT	PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	PROTEIN 4.5 MG/ML IN 20 MM TRIS-HCL PH 8, 100MM NACL, 1MM DTT, 1MM EDTA RESERVOIR 1.75 M SODIUM FORMATE, 0.1 SODIUM CITRATE PH 5.5, 0.15 M POTASSIUM THIOCYANATE VAPOUR DIFFUSION, SITTING DROP, 289 K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.697	α = 103.5
b = 50.76	β = 99.66
c = 74.588	γ = 89.92

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	100	IMAGE PLATE	MARRESEARCH	MIRRORS	2007-08-03	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	2.5	18.99	95.4	0.04	11.9	2.2		23524			48

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	2.5	2.64	93.9		0.11	6.6	2.21

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	PDB ENTRY 2IVT, FLEXIBLE LOOPS REMOVED	2.5	30	22326	1197	95.5	0.20327	0.20114	0.24162	RANDOM	28.346

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]
0.2	0.43	0.63	0.7	1.02	-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.612
r_dihedral_angle_4_deg	18.952
r_dihedral_angle_3_deg	16.289
r_dihedral_angle_1_deg	5.533
r_scangle_it	2.928
r_scbond_it	1.856
r_angle_refined_deg	1.562
r_mcangle_it	1.365
r_mcbond_it	0.79
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.308
r_xyhbond_nbd_refined	0.244
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.201
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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	4327
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	51

Software

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