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Structure of retromer VPS29-VPS35 (483-796) complexed with Fam21A repeat 20 (1289-1302)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8TTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 0.1 M Sodium Citrate pH 4.2, 0.2 M NaCl 16% PEG1000
Crystal Properties Matthews coefficient Solvent content 2.81 56.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.763 α = 90 b = 88.763 β = 90 c = 328.291 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER2 X 16M 2021-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95365 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 3.01 46.9 99.6 0.137 0.143 0.04 0.998 11.7 12.9 27047
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 3.01 3.2 97.9 1.588 1.652 0.451 0.812 13.1
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 3.01 46.58 1.36 26912 1343 99.48 0.2393 0.2376 0.2494 0.2705 0.2685
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 4.731 f_angle_d 1.082 f_chiral_restr 0.06 f_plane_restr 0.007 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7736 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing