9QEK | pdb_00009qek

Structure of Human ROS1 Kinase Domain Harboring the G2032R Solvent-front Mutation in Complex with Zidesamtinib (NVL-520)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UXL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.83	285	0.6 M Potassium Thiocyanate, 0.1 M Citric Acid/Tri-sodium Citrate pH 4.83, 22% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.02	α = 90
b = 106.02	β = 90
c = 50.51	γ = 120

Symmetry
Space Group	P 64

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 EIGER2 X CdTe 16M		2024-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.885603	ESRF	ID23-1

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	2.205	34.703	73.4	0.086	0.093	0.034	0.998	11.2	7.6		12138			78.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.205	2.427	29.7		1.373	1.495	0.585	0.671	1.5	6.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	2.205	34.703	12137	370	73.375	0.203	0.2011	0.2066	0.2722	0.2788	66.337

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]
0.562	0.281		0.562		-1.823

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.922
r_dihedral_angle_6_deg	11.234
r_lrange_other	6.417
r_lrange_it	6.416
r_dihedral_angle_1_deg	5.749
r_scangle_it	3.948
r_scangle_other	3.946
r_dihedral_angle_2_deg	3.917
r_mcangle_it	3.672
r_mcangle_other	3.671
r_scbond_it	2.32
r_scbond_other	2.32
r_mcbond_it	2.198
r_mcbond_other	2.198
r_angle_refined_deg	0.981
r_angle_other_deg	0.327
r_nbd_refined	0.203
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.168
r_nbd_other	0.149
r_xyhbond_nbd_refined	0.146
r_symmetry_nbd_refined	0.102
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.063
r_chiral_restr	0.043
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2217
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	35

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASER	phasing
REFMAC	refinement