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Structural basis of the flanking zinc-finger motifs crucial for the E3 ligase activity of the LNX1 RING domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DIN 5DIN, 3HCT, 1UBQ experimental model PDB 3HCT 5DIN, 3HCT, 1UBQ experimental model PDB 1UBQ 5DIN, 3HCT, 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 298 0.04 M Citric acid, 0.06 M BIS-TRIS propane, pH 6.4, 20% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.6 65.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.372 α = 90 b = 122.372 β = 90 c = 135.199 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL DECTRIS PILATUS 6M-F 2016-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.987 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.48 134.95 99.8 16.1 9.9 15353
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.48 3.81
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 5DIN, 3HCT, 1UBQ 3.49 105.98 12753 1421 92.24 0.24547 0.24085 0.2468 0.28649 0.2893 RANDOM 106.798
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] -0.23 -0.12 -0.23 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.341 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_4_deg 16.504 r_dihedral_angle_1_deg 7.9 r_angle_refined_deg 1.536 r_angle_other_deg 0.986 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.341 r_dihedral_angle_3_deg 19.527 r_dihedral_angle_4_deg 16.504 r_dihedral_angle_1_deg 7.9 r_angle_refined_deg 1.536 r_angle_other_deg 0.986 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5526 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling