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Crystal structure of an 8-repeat consensus TPR superhelix with Copper
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, HANGING DROP 5.5 292 10 mM CuSO4
100 mM NaOAc
30% MPD
Crystal Properties Matthews coefficient Solvent content 3.84 67.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.45 α = 111.47 b = 55.45 β = 111.13 c = 55.52 γ = 105.8
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 2019-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 1.37323 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.6 45.77 94.1 0.137 0.185 0.107 0.959 5.3 2.7 14716
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.74 92.3 0.548 0.751 0.432 0.546 2.7
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 (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 2.6 45.77 13913 783 94.02 0.18198 0.17778 0.1889 0.26124 0.2765 RANDOM 48.493
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] 2.45 0.41 0.06 0.86 -0.87 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 24.149 r_dihedral_angle_3_deg 19.217 r_long_range_B_refined 11.677 r_long_range_B_other 11.677 r_scangle_other 7.697 r_dihedral_angle_1_deg 5.623 r_mcangle_it 4.684 r_mcangle_other 4.683 r_scbond_other 4.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.602 r_dihedral_angle_4_deg 24.149 r_dihedral_angle_3_deg 19.217 r_long_range_B_refined 11.677 r_long_range_B_other 11.677 r_scangle_other 7.697 r_dihedral_angle_1_deg 5.623 r_mcangle_it 4.684 r_mcangle_other 4.683 r_scbond_other 4.66 r_scbond_it 4.648 r_mcbond_it 2.937 r_mcbond_other 2.937 r_angle_refined_deg 1.423 r_angle_other_deg 1.346 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2297 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOSFLM data reduction MOLREP phasing