7OUN | pdb_00007oun

Structure of human PD-L1 in complex with macrocyclic inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O45

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.24	298	0.1M sodium citrate 1.95M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.47	α = 90
b = 86.47	β = 90
c = 86.47	γ = 90

Symmetry
Space Group	P 2 3

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 PILATUS3 6M		2021-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.663	86.47	100	0.091	0.092	0.017	18.1	27.7	17309	17309

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	100		1.576	1.576	1.605	0.301	0.5	28.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5O45	1.9	61.22	16436	873	99.99	0.2331	0.2324	0.24	0.2465	0.25	RANDOM	62.919

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.082
r_dihedral_angle_4_deg	26.596
r_dihedral_angle_3_deg	18.412
r_dihedral_angle_1_deg	8.946
r_angle_refined_deg	2.262
r_angle_other_deg	1.466
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.082
r_dihedral_angle_4_deg	26.596
r_dihedral_angle_3_deg	18.412
r_dihedral_angle_1_deg	8.946
r_angle_refined_deg	2.262
r_angle_other_deg	1.466
r_chiral_restr	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1037
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
iMOSFLM	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.