8AOK

Complex of PD-L1 with VHH6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BIS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1 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 coefficientSolvent content
3.968.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.575α = 90
b = 99.575β = 90
c = 171.515γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2022-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.965459ESRFMASSIF-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.643.199.90.0550.0670.0380.99915.55.656912
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)RedundancyNumber Unique Reflections (All)
11.61.631.1191.3690.7770.5365.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE3BIS1.643.09456884285299.830.1630.16230.184625.702
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]
0.4350.435-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.654
r_dihedral_angle_4_deg16.376
r_dihedral_angle_3_deg13.431
r_lrange_other7.433
r_lrange_it7.431
r_dihedral_angle_1_deg7.017
r_scangle_it5.586
r_scangle_other5.585
r_dihedral_angle_other_2_deg4.944
r_scbond_other3.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.654
r_dihedral_angle_4_deg16.376
r_dihedral_angle_3_deg13.431
r_lrange_other7.433
r_lrange_it7.431
r_dihedral_angle_1_deg7.017
r_scangle_it5.586
r_scangle_other5.585
r_dihedral_angle_other_2_deg4.944
r_scbond_other3.958
r_scbond_it3.957
r_mcangle_other3.347
r_mcangle_it3.342
r_mcbond_it2.482
r_mcbond_other2.481
r_angle_other_deg2.391
r_angle_refined_deg2.138
r_nbd_other0.321
r_symmetry_xyhbond_nbd_refined0.318
r_symmetry_nbd_refined0.236
r_symmetry_nbd_other0.231
r_xyhbond_nbd_refined0.211
r_nbd_refined0.193
r_nbtor_refined0.178
r_symmetry_xyhbond_nbd_other0.101
r_chiral_restr0.098
r_symmetry_nbtor_other0.091
r_xyhbond_nbd_other0.072
r_bond_other_d0.035
r_bond_refined_d0.018
r_gen_planes_other0.017
r_gen_planes_refined0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1903
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms55

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing