4ZQK

Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BIKchain A -3BIK, chain B 3RRQ
experimental modelPDB 3RRQchain A -3BIK, chain B 3RRQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52950.1 M BIS-Tris pH 5.5, 1.84 M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
3.3262.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.862α = 90
b = 70.862β = 90
c = 114.367γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray193PIXELDECTRIS PILATUS 6M2015-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91843BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.4561.3799.980.04335.2210.612737
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.452.5599.920.485.2111.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTchain A -3BIK, chain B 3RRQ2.4561.371208262599.890.20920.20710.2527RANDOM57.568
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]
-0.72-0.36-0.722.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.544
r_dihedral_angle_3_deg17.366
r_dihedral_angle_4_deg12.728
r_dihedral_angle_1_deg7.67
r_mcangle_it4.885
r_mcbond_other3.233
r_mcbond_it3.231
r_angle_refined_deg1.768
r_angle_other_deg0.86
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.544
r_dihedral_angle_3_deg17.366
r_dihedral_angle_4_deg12.728
r_dihedral_angle_1_deg7.67
r_mcangle_it4.885
r_mcbond_other3.233
r_mcbond_it3.231
r_angle_refined_deg1.768
r_angle_other_deg0.86
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1650
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms1

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction