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Zn(II)-bound de novo protein scaffold TFD-EH T87E
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZV9 Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and tryptophan antenna (TFD-EE N6W)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.05 Imidazole, 16% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.11 60.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.24 α = 90 b = 76.24 β = 90 c = 70.25 γ = 120
Symmetry Space Group P 31 2 1
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 2023-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.9763 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 30 96 0.058 9.3 2.9 18249
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2 98.2 0.665 2 3
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 1.9 30 17330 912 96.02 0.18333 0.18149 0.1948 0.21925 0.2337 RANDOM 44.094
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] 0.43 0.22 0.43 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.347 r_dihedral_angle_4_deg 19.012 r_dihedral_angle_3_deg 12.332 r_dihedral_angle_1_deg 5.514 r_long_range_B_refined 4.227 r_long_range_B_other 4.226 r_scangle_other 3.445 r_mcangle_other 3.038 r_mcangle_it 3.035 r_scbond_it 2.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.347 r_dihedral_angle_4_deg 19.012 r_dihedral_angle_3_deg 12.332 r_dihedral_angle_1_deg 5.514 r_long_range_B_refined 4.227 r_long_range_B_other 4.226 r_scangle_other 3.445 r_mcangle_other 3.038 r_mcangle_it 3.035 r_scbond_it 2.565 r_scbond_other 2.564 r_mcbond_it 2.223 r_mcbond_other 2.216 r_angle_refined_deg 1.144 r_angle_other_deg 1.126 r_rigid_bond_restr 0.723 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1304 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing