8VB5 | pdb_00008vb5

Crystal structure of kinase domain of HER2 Exon 20 insertion mutant in complex with tucatinib

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M Bicine pH 8.5, 11% w/v PEG 1500, 0.5mM Tucatinib

Crystal Properties
Matthews coefficient	Solvent content
1.72	28.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.412	α = 90
b = 81.699	β = 90
c = 94.936	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	298	PIXEL	DECTRIS EIGER2 S 9M		2022-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979145	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.48	61.93	99.73	0.044	0.052	0.028	0.999	18.7	6.1		43125

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.518			0.999

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	1.48	61.93	43125	2294	99.7	0.1469	0.1447	0.1521	0.187	0.1877	RANDOM	23.21

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]
0.27			0.26		-0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.499
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	12.696
r_dihedral_angle_1_deg	6.269
r_mcangle_it	1.784
r_mcbond_it	1.389
r_mcbond_other	1.371
r_angle_other_deg	1.304
r_angle_refined_deg	1.297
r_rigid_bond_restr	0.844

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.499
r_dihedral_angle_4_deg	14.744
r_dihedral_angle_3_deg	12.696
r_dihedral_angle_1_deg	6.269
r_mcangle_it	1.784
r_mcbond_it	1.389
r_mcbond_other	1.371
r_angle_other_deg	1.304
r_angle_refined_deg	1.297
r_rigid_bond_restr	0.844
r_chiral_restr	0.07
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2306
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	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.