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NRBF2 coiled coil domain promotes autophagy by strengthening association with Vps15 in the PI3KC3 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other in-house SeMet derivative model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 3.916 M NaCl and 0.1 M Tris buffer (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.67 53.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.529 α = 90 b = 132.81 β = 90 c = 87.29 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289 IMAGE PLATE RIGAKU RAXIS IV++ 2025-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.25 87.29 100 0.051 0.999 33.7 12.4 23604
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 99.8 0.148 12
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT in-house SeMet derivative model 2.25 43.68 22419 1161 99.95 0.21818 0.21583 0.263 0.2733 RANDOM 30.383
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] 0.02 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.077 r_long_range_B_other 8.525 r_long_range_B_refined 8.524 r_dihedral_angle_2_deg 8.077 r_scangle_other 6.98 r_dihedral_angle_1_deg 4.588 r_scbond_it 4.261 r_scbond_other 4.26 r_mcangle_it 3.795 r_mcangle_other 3.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.077 r_long_range_B_other 8.525 r_long_range_B_refined 8.524 r_dihedral_angle_2_deg 8.077 r_scangle_other 6.98 r_dihedral_angle_1_deg 4.588 r_scbond_it 4.261 r_scbond_other 4.26 r_mcangle_it 3.795 r_mcangle_other 3.794 r_mcbond_it 2.615 r_mcbond_other 2.612 r_angle_refined_deg 1.793 r_angle_other_deg 0.583 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2936 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SCALA data scaling PHASER phasing