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Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 6B1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1M HEPES pH 7.0
0.8M Potassium Sodium Tartrate
Crystal Properties Matthews coefficient Solvent content 3 59.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.253 α = 90 b = 97.253 β = 90 c = 128.105 γ = 120
Symmetry Space Group P 63 2 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 2023-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.48 84.224 96.8 0.999 33.5 20.5 50815 27.44
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 1.485 1.584 74.5 0.571 21.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.76 84.224 36124 1728 99.983 0.152 0.1509 0.2347 0.1753 0.2501 24.057
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] -0.545 -0.272 -0.545 1.767
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.09 r_lrange_other 20.698 r_dihedral_angle_6_deg 17.378 r_scangle_it 16.005 r_scangle_other 15.999 r_dihedral_angle_3_deg 12.984 r_scbond_it 11.783 r_scbond_other 11.778 r_mcangle_other 11.628 r_mcangle_it 11.597
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 21.09 r_lrange_other 20.698 r_dihedral_angle_6_deg 17.378 r_scangle_it 16.005 r_scangle_other 15.999 r_dihedral_angle_3_deg 12.984 r_scbond_it 11.783 r_scbond_other 11.778 r_mcangle_other 11.628 r_mcangle_it 11.597 r_mcbond_it 8.702 r_mcbond_other 8.679 r_dihedral_angle_1_deg 8.312 r_rigid_bond_restr 3.388 r_angle_refined_deg 1.362 r_angle_other_deg 0.5 r_symmetry_nbd_refined 0.245 r_nbd_other 0.224 r_nbd_refined 0.2 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1875 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing