5M5E

Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ERJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES, pH 7.0, 2M ammonium sulfate
Crystal Properties
Matthews coefficientSolvent content
4.2571.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.965α = 90
b = 127.965β = 90
c = 135.073γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-12-14MSINGLE 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)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
12.3111.0799.70.178.710.155462

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 REPLACEMENTTHROUGHOUT2erj2.3111.0752650281299.650.200530.198740.23487RANDOM54.882
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]
0.540.270.54-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.098
r_dihedral_angle_4_deg19.698
r_dihedral_angle_3_deg14.162
r_long_range_B_other8.238
r_long_range_B_refined8.237
r_dihedral_angle_1_deg7.319
r_scangle_other4.218
r_mcangle_it3.755
r_mcangle_other3.754
r_scbond_it2.477
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.098
r_dihedral_angle_4_deg19.698
r_dihedral_angle_3_deg14.162
r_long_range_B_other8.238
r_long_range_B_refined8.237
r_dihedral_angle_1_deg7.319
r_scangle_other4.218
r_mcangle_it3.755
r_mcangle_other3.754
r_scbond_it2.477
r_scbond_other2.477
r_mcbond_it2.177
r_mcbond_other2.177
r_angle_refined_deg1.534
r_angle_other_deg0.915
r_chiral_restr0.087
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4271
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SADABSdata scaling
PHASERphasing