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Lys48-linked K48C-diubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AAR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 277 38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
Crystal Properties Matthews coefficient Solvent content 1.91 35.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.79 α = 90 b = 31.191 β = 106.929 c = 25.272 γ = 88.65
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2021-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.25 19.641 95.1 0.062 0.992 6.7 3.6 66682
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 93.6 0.554 0.911 2.7
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.25 19.641 66680 3360 95.071 0.188 0.1861 0.2188 0.272 22.291
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] -1.427 0.758 -0.568 1.236 0.399 0.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 14.018 r_dihedral_angle_3_deg 13.336 r_dihedral_angle_1_deg 7.175 r_lrange_other 5.088 r_lrange_it 5.087 r_scangle_it 4.631 r_scangle_other 4.629 r_mcangle_it 4.607 r_mcangle_other 4.591
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 14.018 r_dihedral_angle_3_deg 13.336 r_dihedral_angle_1_deg 7.175 r_lrange_other 5.088 r_lrange_it 5.087 r_scangle_it 4.631 r_scangle_other 4.629 r_mcangle_it 4.607 r_mcangle_other 4.591 r_scbond_other 3.959 r_scbond_it 3.958 r_mcbond_it 3.836 r_mcbond_other 3.824 r_rigid_bond_restr 3.196 r_angle_refined_deg 1.574 r_angle_other_deg 1.396 r_symmetry_nbd_refined 0.233 r_nbd_other 0.217 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.16 r_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.038 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2400 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing