☰ Navigation Tabs
Structure of retromer VPS26-VPS35 subunits bound to SNX3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FAU 2FAU, 2YPS experimental model PDB 2YPS 2FAU, 2YPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 0.9 M AmSO4, 0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.56 65.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 372.82 α = 90 b = 75.58 β = 97.87 c = 57.53 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 2014-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97893 ALBA XALOC
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 2.69 57 98.3 0.09 0.107 12.09 3.4 85401 -3 67.063
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 2.69 2.85 92.6 0.8 0.951 1.51
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 2FAU, 2YPS 2.7 56.98 39941 2100 95.62 0.2091 0.2072 0.2131 0.2461 0.2462 RANDOM 57.454
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] 0.32 -0.28 0.17 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.791 r_dihedral_angle_4_deg 16.722 r_dihedral_angle_3_deg 13.866 r_dihedral_angle_1_deg 5.953 r_mcangle_it 4.192 r_mcbond_it 2.418 r_mcbond_other 2.417 r_angle_refined_deg 1.198 r_angle_other_deg 0.879 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.791 r_dihedral_angle_4_deg 16.722 r_dihedral_angle_3_deg 13.866 r_dihedral_angle_1_deg 5.953 r_mcangle_it 4.192 r_mcbond_it 2.418 r_mcbond_other 2.417 r_angle_refined_deg 1.198 r_angle_other_deg 0.879 r_chiral_restr 0.067 r_bond_refined_d 0.008 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 7481 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 156
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing