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Crystal structure of TBC domain of human TBC1D17
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Murine TBC1D17 from related entry
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG Smear Broad, 150 mM Li2SO4, 0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.09 60.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.977 α = 90 b = 97.977 β = 90 c = 82.276 γ = 120
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 EIGER X 16M 2024-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97626 PETRA III, EMBL c/o DESY P13 (MX1)
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 3.34 48.99 92.51 0.9986 13.54 10.7 8626
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 3.34 3.63 0.7451
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 3.34 48 7540 1085 67.47 0.22392 0.2146 0.1962 0.28677 0.2421 RANDOM 65.158
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] 2.24 1.12 2.24 -7.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.567 r_dihedral_angle_1_deg 5.867 r_dihedral_angle_2_deg 5.7 r_angle_refined_deg 1.177 r_angle_other_deg 0.422 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.567 r_dihedral_angle_1_deg 5.867 r_dihedral_angle_2_deg 5.7 r_angle_refined_deg 1.177 r_angle_other_deg 0.422 r_chiral_restr 0.056 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4948 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing