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Structural and mechanistic insights into regulation of the retromer coat by TBC1d5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6 289 0.1M Bis-Tris, pH6.0, 2% Tacsimate, pH 6.0, 15~20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.881 α = 90 b = 63.832 β = 90 c = 78.01 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 173 CCD ADSC QUANTUM 315r 2014-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 1 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.5 40 98.12 38 5.7 33729
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 1Z2X 1.5 39.01 33729 1407 98.12 0.14089 0.13905 0.1388 0.18555 0.1846 RANDOM 30.96
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] 0.79 -0.81 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.305 r_sphericity_free 26.526 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_4_deg 11.075 r_sphericity_bonded 8.529 r_dihedral_angle_1_deg 6.577 r_rigid_bond_restr 4.832 r_long_range_B_refined 4.392 r_scangle_other 4.306 r_long_range_B_other 4.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.305 r_sphericity_free 26.526 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_4_deg 11.075 r_sphericity_bonded 8.529 r_dihedral_angle_1_deg 6.577 r_rigid_bond_restr 4.832 r_long_range_B_refined 4.392 r_scangle_other 4.306 r_long_range_B_other 4.218 r_scbond_other 3.959 r_scbond_it 3.957 r_mcangle_it 3.004 r_mcangle_other 3.004 r_mcbond_it 2.523 r_mcbond_other 2.502 r_angle_refined_deg 2.288 r_angle_other_deg 1.201 r_chiral_restr 0.169 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.004 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1672 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing