9I0W | pdb_00009i0w

Structure of human PD-L1 in complex with clinically evaluated inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5J89

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.066	α = 90
b = 72.066	β = 90
c = 89.048	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	100	PIXEL	DECTRIS PILATUS 6M		2024-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.968	ESRF	MASSIF-1

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	2.1	62.41	94.9	0.181	0.218	0.118	0.995	6	5.9		15292

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)
	2.1	2.16	100		1.644	1.966	1.063	0.146	1.1	6.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	36.246	15264	750	94.89	0.237	0.2338	0.2345	0.2995	0.2979	50.11

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]
-1.08	-0.54		-1.08		3.504

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.194
r_dihedral_angle_3_deg	17.159
r_lrange_it	16.937
r_dihedral_angle_6_deg	14.558
r_scangle_it	13.292
r_mcangle_it	10.822
r_scbond_it	9.567
r_dihedral_angle_1_deg	8.421
r_mcbond_it	7.556
r_angle_refined_deg	2.72
r_nbtor_refined	0.293
r_symmetry_nbd_refined	0.272
r_nbd_refined	0.196
r_chiral_restr	0.179
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.145
r_ncsr_local_group_1	0.139
r_gen_planes_refined	0.013
r_bond_refined_d	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1825
Nucleic Acid Atoms
Solvent Atoms	3
Heterogen Atoms	52

Software

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