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Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol
Crystal Properties Matthews coefficient Solvent content 3.53 65.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 371.37 α = 90 b = 75.21 β = 98.56 c = 57.45 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 2015-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97903 SOLEIL PROXIMA 1
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 3.19 56.82 99.3 0.183 0.198 9.3 6.8 26241 -3 63.234
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 3.19 3.38 96.2 0.929 1.006 1.82
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 FREE R-VALUE 5F0J 3.2 56.8 23080 1212 92.57 0.2141 0.2118 0.2166 0.2588 0.2632 RANDOM 61.892
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] 0.13 0.1 -0.2 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 14.932 r_dihedral_angle_3_deg 14.179 r_dihedral_angle_1_deg 6.086 r_mcangle_it 3.85 r_mcbond_it 2.2 r_mcbond_other 2.198 r_angle_refined_deg 1.153 r_angle_other_deg 0.855 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.984 r_dihedral_angle_4_deg 14.932 r_dihedral_angle_3_deg 14.179 r_dihedral_angle_1_deg 6.086 r_mcangle_it 3.85 r_mcbond_it 2.2 r_mcbond_other 2.198 r_angle_refined_deg 1.153 r_angle_other_deg 0.855 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 7480 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 158
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing