8AS0

PD-1 extracellular domain in complex with Fab fragment from D12 antibody

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE MASSIF-1
Synchrotron site	ESRF
Beamline	MASSIF-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-07-01
Detector	DECTRIS PILATUS3 2M
Wavelength(s)	0.965
Spacegroup name	P 1 21 1
Unit cell lengths	81.195, 187.092, 190.845
Unit cell angles	90.00, 90.24, 90.00

Refinement procedure

Resolution	95.420 - 3.500
R-factor	0.2456
Rwork	0.243
R-free	0.29260
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5wt9 Alphafold2
RMSD bond length	0.004
RMSD bond angle	0.700
Data reduction software	XDS
Data scaling software	Aimless
Phasing software	PHASER
Refinement software	PHENIX ((1.20_4459: ???))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	190.840	3.580
High resolution limit [Å]	3.500	3.500
Rmerge	0.141	0.642
Rpim	0.100	0.431
Number of reflections	68755	4708
<I/σ(I)>	3.9
Completeness [%]	96.1	97.6
Redundancy	1.7	1.8
CC(1/2)	0.940	0.431

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	22% PEG 3350, 250 mM sodium malonate, pH 4.5