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Co(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 M Imidazole, 14% PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.15 60.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.36 α = 90 b = 76.36 β = 90 c = 70.81 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 1.95 30 96.2 0.053 13.9 4.1 17125
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 1.95 2.05 98.6 0.513 2.7 4.3
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 1.95 30 16265 856 96.19 0.19129 0.18969 0.1961 0.21944 0.2294 RANDOM 40.626
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 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.547 r_dihedral_angle_4_deg 19.339 r_dihedral_angle_3_deg 13.401 r_dihedral_angle_1_deg 5.708 r_long_range_B_refined 4.282 r_long_range_B_other 4.24 r_scangle_other 3.437 r_mcangle_it 3 r_mcangle_other 2.998 r_scbond_it 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.547 r_dihedral_angle_4_deg 19.339 r_dihedral_angle_3_deg 13.401 r_dihedral_angle_1_deg 5.708 r_long_range_B_refined 4.282 r_long_range_B_other 4.24 r_scangle_other 3.437 r_mcangle_it 3 r_mcangle_other 2.998 r_scbond_it 2.59 r_scbond_other 2.589 r_mcbond_it 2.232 r_mcbond_other 2.227 r_angle_refined_deg 1.19 r_angle_other_deg 1.136 r_rigid_bond_restr 0.84 r_chiral_restr 0.048 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 1313 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing