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Crystal structure of 8-repeat CTPR protein with eliminated coordination sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BU0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 100 mM sodium acetate, pH 5.5, 100 mM CaCl2, 25% MPD
Crystal Properties Matthews coefficient Solvent content 3.03 59.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.26 α = 90 b = 134.185 β = 90 c = 78.096 γ = 90
Symmetry Space Group P 21 21 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 2021-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 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 2.879 67.18 54.9 0.076 0.08 0.023 0.999 16.3 12.7 10700
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 2.879 3.216 1.38 1.454 0.446 0.673 10.4
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 2.88 67.18 10180 520 54.85 0.21195 0.20552 0.2129 0.33834 0.3409 RANDOM 101.651
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] 1.79 -0.53 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.93 r_long_range_B_refined 20.477 r_long_range_B_other 20.475 r_mcangle_other 14.801 r_mcangle_it 14.798 r_scangle_other 14.567 r_mcbond_it 9.33 r_mcbond_other 9.321 r_scbond_it 8.833 r_scbond_other 8.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.93 r_long_range_B_refined 20.477 r_long_range_B_other 20.475 r_mcangle_other 14.801 r_mcangle_it 14.798 r_scangle_other 14.567 r_mcbond_it 9.33 r_mcbond_other 9.321 r_scbond_it 8.833 r_scbond_other 8.831 r_dihedral_angle_1_deg 7.248 r_dihedral_angle_2_deg 4.964 r_angle_refined_deg 1.575 r_angle_other_deg 0.532 r_chiral_restr 0.069 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 4639 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing