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Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 21 (1328-1341)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R17
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.1 M MES pH 6.5, 0.1 M Magnesium Acetate, 10% PEG10,000
Crystal Properties Matthews coefficient Solvent content 2.73 54.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.73 α = 90 b = 165.577 β = 117.51 c = 68 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 EIGER X 16M 2020-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953700 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 3.46 49.31 99.3 0.342 0.37 0.139 0.993 4.5 7 15793
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.46 3.79 97.6 1.233 1.33 0.494 0.762 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.46 48.75 1.33 15694 787 99.09 0.223 0.2214 0.2234 0.2525 0.252
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.238 f_angle_d 1.075 f_chiral_restr 0.059 f_plane_restr 0.008 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7908 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing