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Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176)
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, HANGING DROP 8.5 291 0.1 M NaCl,
20% PEG3350
0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.24 44.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.554 α = 90 b = 138.993 β = 92.78 c = 126.637 γ = 90
Symmetry Space Group P 1 21 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 2017-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979070 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim 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 2.52 126.49 99.8 0.155 0.062 8.5 6.2 68126 39.897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.52 2.56 99.7 1.134 0.455 1.9 6.1
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 2R17 2.52 126.49 64447 3452 99.44 0.2079 0.2048 0.2068 0.2668 0.2638 RANDOM 52.082
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] 0.94 0.26 -0.8 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.393 r_dihedral_angle_4_deg 17.702 r_dihedral_angle_3_deg 16.64 r_dihedral_angle_1_deg 5.734 r_angle_refined_deg 1.244 r_angle_other_deg 0.91 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.393 r_dihedral_angle_4_deg 17.702 r_dihedral_angle_3_deg 16.64 r_dihedral_angle_1_deg 5.734 r_angle_refined_deg 1.244 r_angle_other_deg 0.91 r_chiral_restr 0.069 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 15612 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 48
Software Software Software Name Purpose xia2 data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing