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Crystal structure of the mutant LC3B in complex with p62
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZJD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 297 2 M Ammonium sulphate, 200 mM Potassium sodium tartarate tetrahydrate, 100 mM sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 1.93 36.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.991 α = 90 b = 73.991 β = 90 c = 40.906 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2025-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
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 1.67 35 99.2 0.97 30.24 17.7 14894
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 1.67 1.73 0.79
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 2ZJD 1.67 25.24 14126 732 99.05 0.16904 0.16745 0.1805 0.20256 0.214 RANDOM 26.226
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] -0.22 -0.11 -0.22 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.122 r_long_range_B_refined 7.391 r_long_range_B_other 7.297 r_dihedral_angle_2_deg 6.84 r_dihedral_angle_1_deg 5.772 r_scangle_other 5.17 r_mcangle_it 3.516 r_mcangle_other 3.514 r_scbond_it 3.222 r_scbond_other 3.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.122 r_long_range_B_refined 7.391 r_long_range_B_other 7.297 r_dihedral_angle_2_deg 6.84 r_dihedral_angle_1_deg 5.772 r_scangle_other 5.17 r_mcangle_it 3.516 r_mcangle_other 3.514 r_scbond_it 3.222 r_scbond_other 3.221 r_mcbond_it 2.203 r_mcbond_other 2.203 r_angle_refined_deg 1.824 r_angle_other_deg 0.69 r_chiral_restr 0.11 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 1041 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing