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Terbium(III)-bound de novo TIM barrel-ferredoxin fold fusion dimer with 4-glutamate binding site and tryptophan antenna (TFD-EE N6W)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Single domain Rosetta models
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1 M HEPES pH 7.5, 20 % PEG 4000, and 10 % iso-propanol, containing Gly3 as an additive
Crystal Properties Matthews coefficient Solvent content 2.29 46.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.97 α = 90 b = 56.47 β = 101.69 c = 71.28 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 2M-F 2020-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.85 30 98.4 0.055 0.999 13.12 3.06 56427
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 97.9 0.697 0.845 1.94 2.97
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 Single domain Rosetta models 1.85 30 27802 1463 99.67 0.1958 0.1949 0.1984 0.2285 0.2362 RANDOM 47.312
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] -0.26 0.92 -3.53 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.387 r_dihedral_angle_3_deg 15.032 r_dihedral_angle_4_deg 14.277 r_dihedral_angle_1_deg 5.819 r_angle_refined_deg 1.179 r_angle_other_deg 1.1 r_rigid_bond_restr 0.739 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.387 r_dihedral_angle_3_deg 15.032 r_dihedral_angle_4_deg 14.277 r_dihedral_angle_1_deg 5.819 r_angle_refined_deg 1.179 r_angle_other_deg 1.1 r_rigid_bond_restr 0.739 r_chiral_restr 0.038 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2595 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing