9EO0

Small-Molecule Inhibitors of Programmed Cell Death-1/Programmed Death-Ligand 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1 M Sodium HEPES 7.5 25 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.753	α = 90
b = 75.405	β = 97.249
c = 75.923	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		2023-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.03322	PETRA III, DESY	P11

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	2.5	48.39	99.2	0.148	0.174	0.091	0.997	6.9	7.1		27366

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	2.5	2.6			2.112	2.474	1.278	0.695		7.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	44.393	27351	1380	99.058	0.256	0.253	0.3025	64.368

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]
-0.536		-4.097	3.138		-1.511

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.965
r_dihedral_angle_3_deg	15.974
r_lrange_it	15.452
r_lrange_other	15.451
r_dihedral_angle_6_deg	14.879
r_scangle_it	9.655
r_scangle_other	9.612
r_mcangle_it	9.002
r_mcangle_other	9.002
r_dihedral_angle_1_deg	8.056
r_scbond_it	6.071
r_scbond_other	6.045
r_mcbond_it	5.842
r_mcbond_other	5.818
r_angle_refined_deg	1.766
r_angle_other_deg	0.766
r_xyhbond_nbd_refined	0.349
r_symmetry_nbd_refined	0.216
r_nbd_refined	0.178
r_nbtor_refined	0.163
r_symmetry_nbd_other	0.159
r_nbd_other	0.157
r_ncsr_local_group_9	0.139
r_ncsr_local_group_14	0.137
r_ncsr_local_group_5	0.13
r_ncsr_local_group_8	0.127
r_ncsr_local_group_3	0.126
r_ncsr_local_group_12	0.126
r_ncsr_local_group_4	0.123
r_ncsr_local_group_13	0.122
r_ncsr_local_group_11	0.119
r_ncsr_local_group_2	0.113
r_ncsr_local_group_15	0.112
r_ncsr_local_group_7	0.109
r_ncsr_local_group_6	0.101
r_ncsr_local_group_1	0.099
r_chiral_restr	0.097
r_symmetry_xyhbond_nbd_refined	0.093
r_ncsr_local_group_10	0.089
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.072
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5655
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	146

Software

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