3BIK

Crystal Structure of the PD-1/PD-L1 Complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NPU	PDB ENTRY 1NPU FOR CHAINS B,C, EARLY MODEL FOR CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	20% PEG 3350, 200MM NH4H2PO4, pH 6.00, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.46	α = 90
b = 63.94	β = 90
c = 159.92	γ = 90

Symmetry
Space Group	P 21 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	CCD	SBC-3		2005-04-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

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	2.65	50	98.9	0.075	12.3	6		17320

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	2.65	2.74			0.434		3.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NPU FOR CHAINS B,C, EARLY MODEL FOR CHAIN A	2.65	20	17225	898	98.8	0.214	0.211	0.268	RANDOM	67.59

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]
1.96			-1.41		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.473
r_dihedral_angle_4_deg	17.544
r_dihedral_angle_3_deg	17.421
r_dihedral_angle_1_deg	6.569
r_scangle_it	4.817
r_mcangle_it	4.044
r_scbond_it	2.842
r_mcbond_it	2.322
r_angle_refined_deg	1.4
r_nbtor_refined	0.309
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.207
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.082
r_bond_refined_d	0.014
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3562
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling