8P64 | pdb_00008p64

Co-crystal structure of PD-L1 with low molecular weight inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5C3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	1.2 M S38 sodium citrate tribasic dihydrate 0.01 M sodium borate, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.45	α = 90
b = 73.45	β = 90
c = 96.08	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 PILATUS3 6M		2023-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	3.31	48.04	99.9	0.997	9.39	10.55		4743

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	3.31	3.51			0.423	0.96

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	3.312	38.336	4743	224	99.853	0.237	0.2343	0.23	0.2971	0.29	97.907

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]
-0.052	-0.026		-0.052		0.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.785
r_dihedral_angle_6_deg	17.618
r_lrange_it	17.117
r_lrange_other	17.116
r_dihedral_angle_2_deg	16.027
r_mcangle_it	11.053
r_mcangle_other	11.049
r_scangle_it	10.814
r_scangle_other	10.81
r_dihedral_angle_1_deg	8.334
r_mcbond_it	6.951
r_mcbond_other	6.951
r_scbond_it	6.747
r_scbond_other	6.745
r_angle_refined_deg	1.744
r_angle_other_deg	0.803
r_symmetry_xyhbond_nbd_other	0.365
r_nbd_other	0.323
r_symmetry_xyhbond_nbd_refined	0.315
r_xyhbond_nbd_refined	0.308
r_symmetry_nbd_refined	0.262
r_chiral_restr_other	0.236
r_nbd_refined	0.198
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.171
r_ncsr_local_group_1	0.151
r_chiral_restr	0.102
r_symmetry_nbtor_other	0.085
r_xyhbond_nbd_other	0.036
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.004
r_gen_planes_other	0.004
r_ext_dist_refined_b

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1765
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms	24

Software

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