8G2M | pdb_00008g2m

The tumor activated anti-CTLA-4 monoclonal antibody XTX101 demonstrates tumor-growth inhibition and tumor-selective pharmacodynamics in mouse models of cancer

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.2 M Ammonium Citrate Dibasic pH 5.0, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.18	α = 90
b = 55.23	β = 118.7
c = 73.86	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU HyPix-6000HE		2023-01-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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	1.8	28.98	96.99	0.0645	0.06861	0.0228	0.999	21.67	8.3		42381

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.864			0.5691	0.3137	0.848	2.05

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	1.8	28.98	39463	2120	97.02	0.18155	0.1798	0.19	0.21395	0.22	RANDOM	26.199

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]
0.01		-0.3	-0.18		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.503
r_long_range_B_refined	7.287
r_long_range_B_other	7.162
r_dihedral_angle_1_deg	7.119
r_scangle_other	4.805
r_scbond_it	3.559
r_scbond_other	3.409
r_mcangle_it	2.471
r_mcangle_other	2.471
r_mcbond_it	1.832

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.503
r_long_range_B_refined	7.287
r_long_range_B_other	7.162
r_dihedral_angle_1_deg	7.119
r_scangle_other	4.805
r_scbond_it	3.559
r_scbond_other	3.409
r_mcangle_it	2.471
r_mcangle_other	2.471
r_mcbond_it	1.832
r_mcbond_other	1.827
r_angle_refined_deg	1.282
r_angle_other_deg	0.444
r_chiral_restr	0.067
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3298
Nucleic Acid Atoms
Solvent Atoms	541
Heterogen Atoms	13

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	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.