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A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 1,2-ETHANEDIOL
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.19 α = 90 b = 169.21 β = 90 c = 52.62 γ = 90
Symmetry Space Group P 21 21 2
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 SATURN 2014-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.21 32.2 95 0.06 20.9 5.7 29485
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.26 74.8 0.15 7.8 3.7
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 OTHER THROUGHOUT NONE 2.21 32.02 28823 1536 94.94 0.21857 0.21656 0.2254 0.25541 0.2597 RANDOM 24.191
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] 2.37 -1.18 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_4_deg 21.067 r_dihedral_angle_3_deg 15.543 r_dihedral_angle_1_deg 6.892 r_long_range_B_refined 4.875 r_long_range_B_other 4.875 r_scangle_other 3.548 r_mcangle_it 2.681 r_mcangle_other 2.68 r_scbond_it 2.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.829 r_dihedral_angle_4_deg 21.067 r_dihedral_angle_3_deg 15.543 r_dihedral_angle_1_deg 6.892 r_long_range_B_refined 4.875 r_long_range_B_other 4.875 r_scangle_other 3.548 r_mcangle_it 2.681 r_mcangle_other 2.68 r_scbond_it 2.214 r_scbond_other 2.214 r_mcbond_it 1.713 r_mcbond_other 1.713 r_angle_refined_deg 1.696 r_angle_other_deg 1.042 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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 4524 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling