5J8O

Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82930.2 M ammonium formate and 20% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.313α = 90
b = 55.182β = 90
c = 141.773γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

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
12.347.2699.90.09312.46.812626

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 REPLACEMENTTHROUGHOUT5c3t2.347.261197461099.840.24450.24120.3052RANDOM44.112
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]
2.232.3-4.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.254
r_dihedral_angle_4_deg29.198
r_dihedral_angle_3_deg17.24
r_dihedral_angle_1_deg8.03
r_mcangle_it4.759
r_mcbond_it3.302
r_mcbond_other3.301
r_angle_refined_deg1.878
r_angle_other_deg1.089
r_chiral_restr0.214
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.254
r_dihedral_angle_4_deg29.198
r_dihedral_angle_3_deg17.24
r_dihedral_angle_1_deg8.03
r_mcangle_it4.759
r_mcbond_it3.302
r_mcbond_other3.301
r_angle_refined_deg1.878
r_angle_other_deg1.089
r_chiral_restr0.214
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1906
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms32

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing