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Crystal structure of an 8-repeat consensus TPR superhelix with Gadolinium.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FO7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 292 5mM GdCl3 100 mM Tris HCl
30% MPD
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.228 α = 90 b = 57.73 β = 90 c = 76.289 γ = 90
Symmetry Space Group P 21 21 21
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 Elliptically bent mirror 2020-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.711822 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim 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 1.75 57.73 100 0.106 0.031 0.997 13.2 11.5 20384
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.75 1.84 100 0.687 0.207 0.958 11
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 1.75 46.03 19398 902 99.83 0.18005 0.17873 0.20984 0.246 RANDOM 38.778
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] 5.14 -2.45 -2.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.888 r_dihedral_angle_3_deg 15.125 r_long_range_B_refined 8.548 r_long_range_B_other 8.546 r_scangle_other 7.917 r_dihedral_angle_4_deg 6.455 r_dihedral_angle_1_deg 5.382 r_scbond_it 5.329 r_scbond_other 5.325 r_mcangle_it 4.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.888 r_dihedral_angle_3_deg 15.125 r_long_range_B_refined 8.548 r_long_range_B_other 8.546 r_scangle_other 7.917 r_dihedral_angle_4_deg 6.455 r_dihedral_angle_1_deg 5.382 r_scbond_it 5.329 r_scbond_other 5.325 r_mcangle_it 4.09 r_mcangle_other 4.089 r_mcbond_it 3.263 r_mcbond_other 3.26 r_angle_refined_deg 1.774 r_angle_other_deg 1.554 r_chiral_restr 0.114 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1148 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling autoPROC data reduction MOLREP phasing