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Crystal structure of an 8-repeat consensus TPR superhelix with Lead
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 100mM NaOAc
20mM PbCl2
30% MPD
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.257 α = 90 b = 73.257 β = 90 c = 117.609 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 PILATUS 6M 2020-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.951147 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 1.68 117.609 100 0.276 0.284 0.065 0.993 6.9 18.8 42074
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 1.684 1.713 100 3.89 4.7 0.952 0.701 1 17.1
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 1.68 55.9 39859 2166 99.98 0.20555 0.204 0.2049 0.23401 0.2341 RANDOM 35.415
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 10.817 r_long_range_B_refined 5.215 r_dihedral_angle_1_deg 4.988 r_long_range_B_other 4.988 r_scangle_other 2.416 r_scbond_it 2.389 r_mcangle_it 1.915 r_mcangle_other 1.914
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 10.817 r_long_range_B_refined 5.215 r_dihedral_angle_1_deg 4.988 r_long_range_B_other 4.988 r_scangle_other 2.416 r_scbond_it 2.389 r_mcangle_it 1.915 r_mcangle_other 1.914 r_scbond_other 1.468 r_angle_other_deg 1.198 r_mcbond_it 1.16 r_mcbond_other 1.16 r_angle_refined_deg 1.111 r_chiral_restr 0.053 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2296 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement autoPROC data scaling autoPROC data reduction MOLREP phasing