6I82

Crystal structure of partially phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018412

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M sodium citrate pH 4.5-5.5, 2.0 M sodium formate drop size 500 nl + 500 nl RET at 3 mg/ml in 20 mM Tris pH 8.0, 100 mM NaCl, 1 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.675	α = 90
b = 80.336	β = 99.87
c = 79.74	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M-F		2016-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97949	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.05	45.89	96.4	0.08	1	7.5	3.1		38208

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11	75		0.47	0.73	1.3	2.1

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	2IVS	2.05	45.89	36312	1876	96.33	0.17871	0.17601	0.22928	RANDOM	33.246

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]
2.58		1.11	-1.03		-1.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.956
r_dihedral_angle_4_deg	21.742
r_dihedral_angle_3_deg	16.772
r_long_range_B_refined	7.694
r_long_range_B_other	7.686
r_dihedral_angle_1_deg	6.431
r_scangle_other	5.876
r_mcangle_it	4.217
r_mcangle_other	4.217
r_scbond_it	3.854
r_scbond_other	3.808
r_mcbond_other	2.882
r_mcbond_it	2.881
r_angle_refined_deg	1.645
r_angle_other_deg	1.28
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4569
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	116

Software

Software
Software Name	Purpose
GDA	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
REFMAC	refinement