8P1O | pdb_00008p1o

Solubilizer tag effect on PD-L1/inhibitor binding properties for m-terphenyl derivatives

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	27 % w/v PEG 3350, 0.1 M Bis-Tris propane, pH 7.0 and 0.2 M Lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.088	α = 90
b = 109.991	β = 90
c = 51.823	γ = 90

Symmetry
Space Group	P 21 21 2

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		2021-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	ALBA	XALOC

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	2.17	46.88	99.7	0.144	0.173	0.094	0.993	6.8	6		16333

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	2.17	2.24			0.762	0.905	0.484	0.734		6.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.17	46.88	16297	865	99.597	0.272	0.2708	0.2708	0.2894	0.2894	35.683

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]
0.169			-0.013		-0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.464
r_lrange_it	11.574
r_dihedral_angle_3_deg	11.308
r_dihedral_angle_2_deg	8.859
r_scangle_it	7.622
r_dihedral_angle_1_deg	5.91
r_mcangle_it	5.508
r_scbond_it	5.299
r_mcbond_it	3.837
r_angle_refined_deg	0.983

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.464
r_lrange_it	11.574
r_dihedral_angle_3_deg	11.308
r_dihedral_angle_2_deg	8.859
r_scangle_it	7.622
r_dihedral_angle_1_deg	5.91
r_mcangle_it	5.508
r_scbond_it	5.299
r_mcbond_it	3.837
r_angle_refined_deg	0.983
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.1
r_chiral_restr	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2024
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
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.