9IJT | pdb_00009ijt

Crystal Structure of human Programmed cell death 1 ligand 1 (PD-L1) bound to Small molecule inhibitor Compound-10

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	299	0.1M Tris pH 8.5, 0.1M Magnesium chloride, 25% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.717	α = 90
b = 85.206	β = 90
c = 161.157	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	PIXEL	DECTRIS EIGER X 16M		2022-03-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953732	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.05	45.44	100	0.999	24.6	13.2		36207

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.11			0.958

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	2.05	45.44	36139	1802	99.964	0.233	0.2311	0.2359	0.2601	0.265	48.133

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]
1.157			-0.911		-0.247

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.813
r_dihedral_angle_4_deg	16.03
r_dihedral_angle_3_deg	13.486
r_lrange_it	7.262
r_lrange_other	7.248
r_dihedral_angle_1_deg	6.949
r_scangle_it	2.985
r_scangle_other	2.985
r_mcangle_it	2.706
r_mcangle_other	2.706
r_scbond_it	1.868
r_scbond_other	1.868
r_mcbond_it	1.678
r_mcbond_other	1.678
r_angle_refined_deg	1.504
r_angle_other_deg	1.318
r_symmetry_xyhbond_nbd_refined	0.287
r_nbd_other	0.23
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.204
r_symmetry_nbd_refined	0.183
r_ncsr_local_group_4	0.174
r_nbtor_refined	0.169
r_ncsr_local_group_6	0.169
r_ncsr_local_group_1	0.158
r_ncsr_local_group_3	0.154
r_ncsr_local_group_5	0.154
r_ncsr_local_group_2	0.151
r_symmetry_xyhbond_nbd_other	0.131
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.067
r_chiral_restr_other	0.06
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4032
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	66

Software

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