5LQB

Complex structure of human IL2 mutant, Proleukin, with Fab fragment of NARA1 antibody


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3INK3INK, 3TT1
experimental modelPDB 3TT13INK, 3TT1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320% PEG3350 0.2M Sodium Nitrate
Crystal Properties
Matthews coefficientSolvent content
2.5150.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 201.757α = 90
b = 36.233β = 102.93
c = 88.707γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2015-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.9558.7484.80.0660.07914.23.239422
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952960.3942.593.22

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 REPLACEMENTTHROUGHOUT3INK, 3TT11.9558.7437450197284.860.194350.189140.29083RANDOM42.434
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]
-0.07-0.460.67-0.35
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free81.658
r_sphericity_bonded39.003
r_dihedral_angle_2_deg37.328
r_dihedral_angle_4_deg19.9
r_dihedral_angle_3_deg18.272
r_long_range_B_refined13.276
r_long_range_B_other12.065
r_scangle_other9.312
r_mcangle_it9.128
r_mcangle_other9.126
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free81.658
r_sphericity_bonded39.003
r_dihedral_angle_2_deg37.328
r_dihedral_angle_4_deg19.9
r_dihedral_angle_3_deg18.272
r_long_range_B_refined13.276
r_long_range_B_other12.065
r_scangle_other9.312
r_mcangle_it9.128
r_mcangle_other9.126
r_scbond_it8.295
r_scbond_other8.267
r_dihedral_angle_1_deg7.66
r_mcbond_it7.638
r_mcbond_other7.638
r_rigid_bond_restr4.011
r_angle_refined_deg2.084
r_angle_other_deg1.162
r_chiral_restr0.133
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4329
Nucleic Acid Atoms
Solvent Atoms494
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing