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Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ERJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M HEPES, pH 7.0, 2M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.25 71.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.965 α = 90 b = 127.965 β = 90 c = 135.073 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.3 111.07 99.7 0.17 8.7 10.1 55462
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2erj 2.3 111.07 52650 2812 99.65 0.20053 0.19874 0.2037 0.23487 0.2379 RANDOM 54.882
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] 0.54 0.27 0.54 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.098 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_3_deg 14.162 r_long_range_B_other 8.238 r_long_range_B_refined 8.237 r_dihedral_angle_1_deg 7.319 r_scangle_other 4.218 r_mcangle_it 3.755 r_mcangle_other 3.754 r_scbond_it 2.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.098 r_dihedral_angle_4_deg 19.698 r_dihedral_angle_3_deg 14.162 r_long_range_B_other 8.238 r_long_range_B_refined 8.237 r_dihedral_angle_1_deg 7.319 r_scangle_other 4.218 r_mcangle_it 3.755 r_mcangle_other 3.754 r_scbond_it 2.477 r_scbond_other 2.477 r_mcbond_it 2.177 r_mcbond_other 2.177 r_angle_refined_deg 1.534 r_angle_other_deg 0.915 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 4271 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement XDS data reduction SADABS data scaling PHASER phasing