3FN3

Dimeric Structure of PD-L1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529115% PEG 3350 (w/v), 0.2M ammonium acetate (NH4Ac), 0.1M BIS-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2745.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.865α = 90
b = 91.373β = 90
c = 140.316γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IV++2008-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.65091.15.736104196032
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.798.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3BIS2.71521201164597.620.229080.225670.29614RANDOM58.811
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]
1.8-4.592.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.277
r_dihedral_angle_3_deg21.309
r_dihedral_angle_4_deg17.326
r_dihedral_angle_1_deg7.416
r_scangle_it2.595
r_angle_refined_deg1.734
r_scbond_it1.686
r_mcangle_it1.316
r_mcbond_it0.742
r_symmetry_hbond_refined0.352
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.277
r_dihedral_angle_3_deg21.309
r_dihedral_angle_4_deg17.326
r_dihedral_angle_1_deg7.416
r_scangle_it2.595
r_angle_refined_deg1.734
r_scbond_it1.686
r_mcangle_it1.316
r_mcbond_it0.742
r_symmetry_hbond_refined0.352
r_nbtor_refined0.318
r_symmetry_vdw_refined0.256
r_nbd_refined0.254
r_xyhbond_nbd_refined0.197
r_chiral_restr0.116
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3428
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling