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Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OLM 5OLM, 5EYA experimental model PDB 5EYA 5OLM, 5EYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 Crystals grew in 0.1 M Tris/BICINE pH 8.5, 10.5 % (w/v) PEG3350/PEG 1K/MPD and 0.08 M sodium nitrate/sodium phosphate/ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.75 α = 89.9 b = 83.31 β = 89.05 c = 86.75 γ = 88.7
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 2018-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.8 19.76 95.74 0.03857 0.05454 0.03857 0.998 12.83 1.8 32828
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 0.3994 0.5649 0.3994 0.735
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5OLM, 5EYA 2.8 19.76 32828 2003 95.74 0.2092 0.2113 0.2495 0.2494 RANDOM 79.03
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] 2.1 1.96 -0.31 -0.84 2.67 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.251 r_dihedral_angle_4_deg 14.605 r_dihedral_angle_3_deg 13.489 r_long_range_B_refined 11.413 r_long_range_B_other 11.412 r_scangle_other 8.56 r_mcangle_it 7.985 r_mcangle_other 7.985 r_scbond_it 5.569 r_scbond_other 5.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.251 r_dihedral_angle_4_deg 14.605 r_dihedral_angle_3_deg 13.489 r_long_range_B_refined 11.413 r_long_range_B_other 11.412 r_scangle_other 8.56 r_mcangle_it 7.985 r_mcangle_other 7.985 r_scbond_it 5.569 r_scbond_other 5.568 r_dihedral_angle_1_deg 5.538 r_mcbond_it 5.228 r_mcbond_other 5.226 r_angle_refined_deg 1.259 r_angle_other_deg 0.827 r_chiral_restr 0.054 r_bond_refined_d 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9443 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing