5J8O | pdb_00005j8o

Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.2 M ammonium formate and 20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.313	α = 90
b = 55.182	β = 90
c = 141.773	γ = 90

Symmetry
Space Group	P 2 21 21

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		2015-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918409	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.3	47.26	99.9	0.093	12.4	6.8		12626

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	5c3t	2.3	47.26	11974	610	99.84	0.2445	0.2412	0.24	0.3052	0.3	RANDOM	44.112

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]
2.23			2.3		-4.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.254
r_dihedral_angle_4_deg	29.198
r_dihedral_angle_3_deg	17.24
r_dihedral_angle_1_deg	8.03
r_mcangle_it	4.759
r_mcbond_it	3.302
r_mcbond_other	3.301
r_angle_refined_deg	1.878
r_angle_other_deg	1.089
r_chiral_restr	0.214

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.254
r_dihedral_angle_4_deg	29.198
r_dihedral_angle_3_deg	17.24
r_dihedral_angle_1_deg	8.03
r_mcangle_it	4.759
r_mcbond_it	3.302
r_mcbond_other	3.301
r_angle_refined_deg	1.878
r_angle_other_deg	1.089
r_chiral_restr	0.214
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1906
Nucleic Acid Atoms
Solvent Atoms	30
Heterogen Atoms	32

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
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.