☰ Navigation Tabs
Metal-free de novo protein scaffold TFD-EH
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 0.1 M Potassium Citrate, 20% PEG 3350,
Crystal Properties Matthews coefficient Solvent content 3.13 60.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.67 α = 90 b = 78.67 β = 90 c = 66.26 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 2021-08-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.6 30 99.1 0.039 20.3 6.1 31409
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 1.6 1.7 99.4 0.587 2.7 5.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 30 29824 1569 99.18 0.15813 0.1568 0.18393 0.2083 RANDOM 32.197
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] 0.19 0.1 0.19 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.616 r_dihedral_angle_4_deg 20.838 r_dihedral_angle_3_deg 11.672 r_dihedral_angle_1_deg 6.067 r_long_range_B_refined 3.041 r_long_range_B_other 2.651 r_scangle_other 2.05 r_mcangle_it 1.654 r_mcangle_other 1.653 r_scbond_other 1.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.616 r_dihedral_angle_4_deg 20.838 r_dihedral_angle_3_deg 11.672 r_dihedral_angle_1_deg 6.067 r_long_range_B_refined 3.041 r_long_range_B_other 2.651 r_scangle_other 2.05 r_mcangle_it 1.654 r_mcangle_other 1.653 r_scbond_other 1.593 r_scbond_it 1.592 r_mcbond_it 1.242 r_mcbond_other 1.239 r_angle_other_deg 1.214 r_angle_refined_deg 1.129 r_rigid_bond_restr 0.553 r_chiral_restr 0.052 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 1320 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing