8EQ6

PD1 signaling receptor bound to FAB Complex

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.744	α = 90
b = 78.51	β = 106.423
c = 102.021	γ = 90

Symmetry
Space Group	C 1 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	100	PIXEL	DECTRIS EIGER2 X 16M		2022-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.65	49.62	98.9	0.156	0.169	0.066	0.994	4.86	6.3		60066			15.86

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	1.65	1.68	86.2		2.329	2.657	1.246	0.338	0.2	4.1

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 (All)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6k0y	1.65	49.616	60052	3020	98.926	0.23	0.2278	0.2642	RANDOM	25.019

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]
0.359		0.404	0.601		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.298
r_dihedral_angle_3_deg	16
r_dihedral_angle_1_deg	8.077
r_dihedral_angle_2_deg	7.661
r_lrange_it	5.894
r_lrange_other	5.88
r_scangle_it	4.605
r_scangle_other	4.604
r_mcangle_it	3.329
r_mcangle_other	3.329
r_scbond_it	3.126
r_scbond_other	3.125
r_mcbond_it	2.306
r_mcbond_other	2.306
r_angle_refined_deg	1.599
r_angle_other_deg	0.54
r_symmetry_nbd_refined	0.242
r_nbd_refined	0.212
r_symmetry_nbd_other	0.205
r_nbd_other	0.195
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.154
r_symmetry_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_other	0.11
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_chiral_restr_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3877
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms

Software

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