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Crystal structure of TBC domain of murine TBC1D17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 30% Precipitant mix (20% PEG 3350, 20% PEG 1000, 20% MPD), 50 mM MgCl2, 50 mM CaCl2, 0.1M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.241 α = 90 b = 160.895 β = 90 c = 41.897 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 EIGER2 X 16M 2023-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.2 46.66 96.7 0.996 8.03 3.44 32171
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 0.648
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 2.2 46.66 30535 1636 96.77 0.183 0.17925 0.1936 0.2528 0.2593 RANDOM 44.573
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] -1.78 2.83 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.955 r_long_range_B_refined 7.725 r_long_range_B_other 7.723 r_dihedral_angle_2_deg 7.381 r_dihedral_angle_1_deg 5.259 r_scangle_other 5.009 r_mcangle_it 4.507 r_mcangle_other 4.507 r_scbond_it 3.017 r_scbond_other 3.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.955 r_long_range_B_refined 7.725 r_long_range_B_other 7.723 r_dihedral_angle_2_deg 7.381 r_dihedral_angle_1_deg 5.259 r_scangle_other 5.009 r_mcangle_it 4.507 r_mcangle_other 4.507 r_scbond_it 3.017 r_scbond_other 3.017 r_mcbond_it 2.784 r_mcbond_other 2.783 r_angle_refined_deg 1.978 r_angle_other_deg 0.722 r_chiral_restr 0.092 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 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 5301 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing