7DU9 | pdb_00007du9

Crystal structure of human Proto-oncogene tyrosine-protein kinase receptor Ret in complex with Pralsetinib

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293.15	0.20 M LiCl, 0.10 M Na Acetate, pH 4.50, 2.5 M Na Formate, 5 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.887	α = 90
b = 80.577	β = 99.72
c = 79.866	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		2019-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9999	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	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	2.31	78.72	97.1	0.094	0.119	10.45	2.7		27199

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.31	2.56	97.7		0.44	0.551		2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.31	78.72	26013	1185	97.15	0.2204	0.219	0.22	0.249	0.24	RANDOM	39.012

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]
1.54		0.15	-0.47		-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.635
r_dihedral_angle_4_deg	15.156
r_dihedral_angle_3_deg	14.102
r_dihedral_angle_1_deg	6.315
r_angle_refined_deg	1.551
r_angle_other_deg	1.229
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.635
r_dihedral_angle_4_deg	15.156
r_dihedral_angle_3_deg	14.102
r_dihedral_angle_1_deg	6.315
r_angle_refined_deg	1.551
r_angle_other_deg	1.229
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4478
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	86

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.