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Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 0.1 M sodium chloride
0.1 M Tris pH 8.0
4-8% PEG6000.
Crystal Properties Matthews coefficient Solvent content 5.4 77.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.201 α = 90 b = 173.243 β = 90 c = 445.775 γ = 90
Symmetry Space Group P 21 21 21
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-F 2016-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9791 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3 222.89 99 0.094 0.101 0.999 12.6 6.954 93761 -3 104.762
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.19 97.8 2.315 2.517 0.341 0.74 6.546
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 4.3 222.89 46155 2460 99.95 0.2566 0.2537 0.2486 0.3109 0.2957 RANDOM 260.86
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] -3.09 -0.79 3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.341 r_dihedral_angle_3_deg 18.834 r_dihedral_angle_4_deg 12.229 r_dihedral_angle_1_deg 7.23 r_angle_refined_deg 1.374 r_angle_other_deg 0.98 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.341 r_dihedral_angle_3_deg 18.834 r_dihedral_angle_4_deg 12.229 r_dihedral_angle_1_deg 7.23 r_angle_refined_deg 1.374 r_angle_other_deg 0.98 r_chiral_restr 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22276 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction autoSHARP phasing