☰ Navigation Tabs
Crystal structure of unbranched mixed tri-Ubiquitin chain containing K48 and K63 linkages.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B08
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.3M MgSo4 and 100mM MES monohydrate pH 6.5
Crystal Properties Matthews coefficient Solvent content 7.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.767 α = 90 b = 110.767 β = 90 c = 417.004 γ = 120
Symmetry Space Group P 61 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 100 PIXEL DECTRIS PILATUS 6M-F 2015-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 1.0080 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.14 104.25 100 0.142 9.7 11.4 27681
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.14 3.33 100 2.081 0.675 0.9 10 4350
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 3B08 3.14 95.93 26195 1362 99.82 0.21866 0.21691 0.2229 0.25405 0.2571 RANDOM 135.247
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] 4.72 2.36 4.72 -15.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.129 r_long_range_B_refined 22.985 r_dihedral_angle_3_deg 22.542 r_dihedral_angle_4_deg 21.956 r_mcangle_it 16.092 r_scbond_it 15.543 r_mcbond_it 11.705 r_dihedral_angle_1_deg 5.894 r_angle_refined_deg 2.376 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.129 r_long_range_B_refined 22.985 r_dihedral_angle_3_deg 22.542 r_dihedral_angle_4_deg 21.956 r_mcangle_it 16.092 r_scbond_it 15.543 r_mcbond_it 11.705 r_dihedral_angle_1_deg 5.894 r_angle_refined_deg 2.376 r_chiral_restr 0.129 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3594 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing DM phasing XDS data reduction