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Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.52 65.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 371.29 α = 90 b = 75.32 β = 97.66 c = 57.27 γ = 90
Symmetry Space Group C 1 2 1
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 2015-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97895 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.77 56.761 99.1 0.066 0.078 0.999 12.17 77507 -3 80.168
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.77 2.94 95.3 0.904 1.073 0.808 1.33
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 5F0L 2.78 56.76 36032 1901 95.13 0.2209 0.2189 0.2249 0.2605 0.2597 RANDOM 70.57
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] -0.04 -0.73 0.09 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_4_deg 14.651 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_1_deg 5.79 r_mcangle_it 4.414 r_mcbond_it 2.512 r_mcbond_other 2.512 r_angle_refined_deg 1.135 r_angle_other_deg 0.851 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_4_deg 14.651 r_dihedral_angle_3_deg 13.526 r_dihedral_angle_1_deg 5.79 r_mcangle_it 4.414 r_mcbond_it 2.512 r_mcbond_other 2.512 r_angle_refined_deg 1.135 r_angle_other_deg 0.851 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7453 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 135
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing