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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
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.1 M MES monohydrate pH 6.0, 0.05 M calcium chloride dihydrate, 45 % polyethylene glycol 200
Crystal Properties Matthews coefficient Solvent content 3.53 65.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.375 α = 90 b = 92.375 β = 90 c = 84.41 γ = 120
Symmetry Space Group P 62 2 2
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 1.51 79.884 99.1 19.8 17.6 31064
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 1.51 1.54
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 1.7 79.884 21825 1998 99.14 0.18162 0.17847 0.1861 0.21528 0.2258 RANDOM 29.799
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] -1.73 -0.87 -1.73 5.63
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.253 r_dihedral_angle_2_deg 30.335 r_sphericity_bonded 17.776 r_dihedral_angle_3_deg 13.238 r_dihedral_angle_4_deg 9.053 r_scangle_other 7.679 r_long_range_B_refined 7.668 r_long_range_B_other 7.557 r_scbond_it 6.999 r_scbond_other 6.996
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 33.253 r_dihedral_angle_2_deg 30.335 r_sphericity_bonded 17.776 r_dihedral_angle_3_deg 13.238 r_dihedral_angle_4_deg 9.053 r_scangle_other 7.679 r_long_range_B_refined 7.668 r_long_range_B_other 7.557 r_scbond_it 6.999 r_scbond_other 6.996 r_dihedral_angle_1_deg 6.093 r_mcbond_it 5.696 r_mcbond_other 5.688 r_mcangle_it 5.683 r_mcangle_other 5.682 r_angle_refined_deg 2.295 r_rigid_bond_restr 1.338 r_angle_other_deg 1.045 r_chiral_restr 0.077 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 983 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling