9DOM | pdb_00009dom

PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BQV
experimental model	PDB	7LPS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.395	α = 90
b = 69.239	β = 90.01
c = 79.857	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	95	PIXEL	DECTRIS EIGER2 X 16M		2022-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03

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	1.69	79.86	84.8	0.077	0.998	13.3	6.4		46939

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	1.69	1.72			0.653	0.826		4.9

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	1.69	79.86	44747	2166	84.64	0.21164	0.21053	0.2164	0.2342	0.2418	RANDOM	22.825

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]
0.19		-0.02	-0.29		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	20.999
r_dihedral_angle_3_deg	14.924
r_dihedral_angle_1_deg	6.35
r_long_range_B_refined	5.4
r_long_range_B_other	5.376
r_scangle_other	3.671
r_mcangle_it	2.988
r_mcangle_other	2.988
r_scbond_it	2.385
r_scbond_other	2.385
r_mcbond_it	2.015
r_mcbond_other	2.012
r_angle_refined_deg	1.901
r_angle_other_deg	0.503
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4211
Nucleic Acid Atoms
Solvent Atoms	277
Heterogen Atoms	140

Software

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