☰ Navigation Tabs
Structure of the IL-2 Surrogate Cytokine Agonist DR638
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 10% (v/v) glycerol, 0.1 M HEPES pH 7.5, 30% (v/v) PEG 400 and 5% (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.52 51.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.205 α = 90 b = 63.135 β = 90 c = 87.451 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 16M 2024-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.8 38.81 99.6 0.067 0.077 0.036 0.998 12.8 4.5 25844
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.9 0.774 0.889 0.43 0.749 4.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 38.8 24498 1296 99.48 0.18164 0.17998 0.1911 0.21114 0.2156 RANDOM 23.983
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] -2.1 -0.88 2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.755 r_dihedral_angle_2_deg 11.443 r_long_range_B_refined 8.155 r_long_range_B_other 8.008 r_dihedral_angle_1_deg 6.684 r_scangle_other 6.029 r_scbond_it 4.052 r_scbond_other 4.05 r_mcangle_it 3.467 r_mcangle_other 3.465
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.755 r_dihedral_angle_2_deg 11.443 r_long_range_B_refined 8.155 r_long_range_B_other 8.008 r_dihedral_angle_1_deg 6.684 r_scangle_other 6.029 r_scbond_it 4.052 r_scbond_other 4.05 r_mcangle_it 3.467 r_mcangle_other 3.465 r_mcbond_it 2.43 r_mcbond_other 2.414 r_angle_refined_deg 1.767 r_angle_other_deg 0.617 r_chiral_restr 0.09 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1820 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction