☰ Navigation Tabs
Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (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, 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.5 64.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 369.48 α = 90 b = 74.91 β = 97.64 c = 57.39 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 2015-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9750 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.1 56.89 99.7 0.105 0.124 8.57 3.5 55451 -3 79.095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.28 99.1 0.883 1.043 1.3
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 3.1 56.89 25885 1361 95.62 0.212 0.2098 0.214 0.2537 0.2589 RANDOM 83.908
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] 0.11 -0.36 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.882 r_dihedral_angle_3_deg 13.752 r_dihedral_angle_4_deg 13.673 r_dihedral_angle_1_deg 6.023 r_mcangle_it 5.351 r_mcbond_it 3.139 r_mcbond_other 3.139 r_angle_refined_deg 1.161 r_angle_other_deg 0.852 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.882 r_dihedral_angle_3_deg 13.752 r_dihedral_angle_4_deg 13.673 r_dihedral_angle_1_deg 6.023 r_mcangle_it 5.351 r_mcbond_it 3.139 r_mcbond_other 3.139 r_angle_refined_deg 1.161 r_angle_other_deg 0.852 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 7436 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing