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Crystal structure of an 8-repeat consensus TPR superhelix with Calcium (low concentration)
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 CaCl2, 10 mM
100 mM NaOAc, pH 5.5
30% MPD
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.448 α = 90 b = 70.249 β = 90 c = 102.619 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 2018-02-02 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) 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 1.7 70.25 99.9 0.101 0.041 0.995 7.9 5.8 53530
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) 1.7 1.79 100 1.392 0.571 0.477 5.8
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 1.7 57.97 50674 2665 99.6 0.20311 0.20126 0.2094 0.23897 0.2457 RANDOM 40.298
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_3_deg 17.113 r_dihedral_angle_4_deg 9.384 r_long_range_B_refined 8.52 r_long_range_B_other 8.52 r_scangle_other 6.984 r_dihedral_angle_1_deg 5.019 r_scbond_it 4.588 r_scbond_other 4.587 r_mcangle_it 4.434
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.331 r_dihedral_angle_3_deg 17.113 r_dihedral_angle_4_deg 9.384 r_long_range_B_refined 8.52 r_long_range_B_other 8.52 r_scangle_other 6.984 r_dihedral_angle_1_deg 5.019 r_scbond_it 4.588 r_scbond_other 4.587 r_mcangle_it 4.434 r_mcangle_other 4.433 r_mcbond_it 3.5 r_mcbond_other 3.457 r_angle_refined_deg 1.545 r_angle_other_deg 1.465 r_chiral_restr 0.094 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 3427 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement SCALA data scaling iMOSFLM data reduction MOLREP phasing