4ZQK | pdb_00004zqk

Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BIK	chain A -3BIK, chain B 3RRQ
experimental model	PDB	3RRQ	chain A -3BIK, chain B 3RRQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	0.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.862	α = 90
b = 70.862	β = 90
c = 114.367	γ = 120

Symmetry
Space Group	P 31 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	193	PIXEL	DECTRIS PILATUS 6M		2015-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91843	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	2.45	61.37	99.98	0.043	35.22	10.6		12737

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.55	99.92		0.48	5.21	11.2

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	chain A -3BIK, chain B 3RRQ	2.45	61.37	12082	625	99.89	0.2092	0.2071	0.21	0.2527	0.26	RANDOM	57.568

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]
-0.72	-0.36		-0.72		2.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.544
r_dihedral_angle_3_deg	17.366
r_dihedral_angle_4_deg	12.728
r_dihedral_angle_1_deg	7.67
r_mcangle_it	4.885
r_mcbond_other	3.233
r_mcbond_it	3.231
r_angle_refined_deg	1.768
r_angle_other_deg	0.86
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.544
r_dihedral_angle_3_deg	17.366
r_dihedral_angle_4_deg	12.728
r_dihedral_angle_1_deg	7.67
r_mcangle_it	4.885
r_mcbond_other	3.233
r_mcbond_it	3.231
r_angle_refined_deg	1.768
r_angle_other_deg	0.86
r_chiral_restr	0.1
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1650
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms	1

Software

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

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.