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Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a
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, SITTING DROP 7.4 293 20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4
Crystal Properties Matthews coefficient Solvent content 2.58 52.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.5 α = 90 b = 140.83 β = 90 c = 141.34 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 2021-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91788 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 19.919 99.7 0.999 16.1 13.6 40494
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 0.597
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 19.919 40436 2021 99.729 0.205 0.2017 0.2045 0.2639 0.2678 115.59
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] 5.565 -3.074 -2.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.753 r_dihedral_angle_3_deg 17.184 r_dihedral_angle_6_deg 13.914 r_lrange_it 13.71 r_lrange_other 13.71 r_scangle_it 10.748 r_scangle_other 10.747 r_mcangle_it 9.957 r_mcangle_other 9.956 r_scbond_it 7.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 18.753 r_dihedral_angle_3_deg 17.184 r_dihedral_angle_6_deg 13.914 r_lrange_it 13.71 r_lrange_other 13.71 r_scangle_it 10.748 r_scangle_other 10.747 r_mcangle_it 9.957 r_mcangle_other 9.956 r_scbond_it 7.041 r_scbond_other 7.041 r_mcbond_it 6.839 r_mcbond_other 6.839 r_dihedral_angle_1_deg 5.848 r_angle_refined_deg 1.444 r_angle_other_deg 0.804 r_nbd_other 0.336 r_nbd_refined 0.224 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.177 r_xyhbond_nbd_refined 0.14 r_ncsr_local_group_2 0.113 r_symmetry_xyhbond_nbd_refined 0.103 r_ncsr_local_group_1 0.097 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.008 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7729 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing