7XYQ

Crystal strucutre of PD-L1 and the computationally designed DBL1_03 protein binder


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION2910.02 M nickel (II) chloride hexahydrate, 0.02 M magnesium chloride hexahydrate, 0.02 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate, pH4.5, 24% w/v polyethylene glycol monomethylether 2000
Crystal Properties
Matthews coefficientSolvent content
3.3558.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.93α = 90
b = 97.93β = 90
c = 106.11γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2019-01-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97889SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.8548.9799.90.1410.99820.725.4125911.36124.12
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.951003.1260.5541.126.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.8548.971.351258263099.930.30060.29960.3182124.12
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d6.8549
f_angle_d1.254
f_chiral_restr0.0617
f_bond_d0.0099
f_plane_restr0.0095
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2619
Nucleic Acid Atoms
Solvent Atoms1
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing