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Crystal structure of TRIM21 E3 ligase, RING domain in complex with its cognate E2 conjugating enzyme UBE2E1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 100mM Bicine pH 9.0 and 5% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 3.1 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.835 α = 90 b = 95.871 β = 93.15 c = 235.097 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS 6M 2014-08-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.278383 BESSY 14.1
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 2.82 47.9 91.2 0.076 0.082 0.031 0.999 17 6.81 51064
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 2.82 2.912 50.9 1.05 1.13 0.42 0.705 1.8 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.82 47.9 48491 2549 91.19 0.25492 0.25283 0.2554 0.29407 0.2941 RANDOM 90.688
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] 0.89 -0.56 0.54 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.378 r_dihedral_angle_4_deg 18.836 r_long_range_B_refined 18.301 r_long_range_B_other 18.299 r_dihedral_angle_3_deg 17.144 r_mcangle_it 10.455 r_mcangle_other 10.454 r_scangle_other 9.504 r_mcbond_it 6.483 r_mcbond_other 6.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.378 r_dihedral_angle_4_deg 18.836 r_long_range_B_refined 18.301 r_long_range_B_other 18.299 r_dihedral_angle_3_deg 17.144 r_mcangle_it 10.455 r_mcangle_other 10.454 r_scangle_other 9.504 r_mcbond_it 6.483 r_mcbond_other 6.479 r_scbond_it 5.681 r_scbond_other 5.681 r_dihedral_angle_1_deg 4.413 r_angle_refined_deg 1.467 r_angle_other_deg 1.309 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 13057 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling SHELXCD phasing Coot model building