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De novo single-chain immunoglobulin dimer scIg12+EF3a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Model prediction
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 PEG MME 2000 20.0%w/v, TRIS 0.1M pH 7.0
Crystal Properties Matthews coefficient Solvent content 4.07 69.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.841 α = 90 b = 73.841 β = 90 c = 96.245 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 6M 2022-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.50102 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 58.59 100 0.016 0.944 15.4 16.2 7030
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 0.876
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 Model prediction 2.8 58.59 6261 724 99.9 0.20744 0.20182 0.21 0.25711 0.256 RANDOM 94.072
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] 0.6 0.6 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_dihedral_angle_3_deg 21.366 r_dihedral_angle_4_deg 19.151 r_scangle_other 15.814 r_mcangle_it 12.055 r_mcangle_other 11.969 r_scbond_it 10.719 r_scbond_other 10.715 r_dihedral_angle_1_deg 8.836 r_mcbond_it 8.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.563 r_dihedral_angle_3_deg 21.366 r_dihedral_angle_4_deg 19.151 r_scangle_other 15.814 r_mcangle_it 12.055 r_mcangle_other 11.969 r_scbond_it 10.719 r_scbond_other 10.715 r_dihedral_angle_1_deg 8.836 r_mcbond_it 8.38 r_mcbond_other 8.27 r_angle_refined_deg 1.675 r_angle_other_deg 1.122 r_chiral_restr 0.063 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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 1135 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction MOLREP phasing