8AOK | pdb_00008aok

Complex of PD-L1 with VHH6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.1 M HEPES:MOPS, pH 7.5, 0.02 M Ammonium acetate, 0.02 M Potassium sodium tartrate tetrahydrate, 0.02 M Sodium citrate tribasic dihydrate, 0.02 M Sodium formate, 0.02M Sodium oxamate, 10% (w/v) PEG 20000 and 20% (v/v) PEG 500-MME.

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.575	α = 90
b = 99.575	β = 90
c = 171.515	γ = 90

Symmetry
Space Group	I 41 2 2

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 2M		2022-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	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	1.6	43.1	99.9	0.055	0.067	0.038	0.999	15.5	5.6		56912

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	1.6	1.63			1.119	1.369	0.777	0.536		5.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3BIS	1.6	43.094	56884	2852	99.83	0.163	0.1623	0.17	0.1846	0.19	25.702

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]
0.435			0.435		-0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.654
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	13.431
r_lrange_other	7.433
r_lrange_it	7.431
r_dihedral_angle_1_deg	7.017
r_scangle_it	5.586
r_scangle_other	5.585
r_dihedral_angle_other_2_deg	4.944
r_scbond_other	3.958
r_scbond_it	3.957
r_mcangle_other	3.347
r_mcangle_it	3.342
r_mcbond_it	2.482
r_mcbond_other	2.481
r_angle_other_deg	2.391
r_angle_refined_deg	2.138
r_nbd_other	0.321
r_symmetry_xyhbond_nbd_refined	0.318
r_symmetry_nbd_refined	0.236
r_symmetry_nbd_other	0.231
r_xyhbond_nbd_refined	0.211
r_nbd_refined	0.193
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_other	0.101
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.091
r_xyhbond_nbd_other	0.072
r_bond_other_d	0.035
r_bond_refined_d	0.018
r_gen_planes_other	0.017
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1903
Nucleic Acid Atoms
Solvent Atoms	311
Heterogen Atoms	55

Software

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