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Cyclic Lys48-linked triubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.4 293 20% PEG 3350, 200 mM zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.43 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.429 α = 90 b = 54.82 β = 121.99 c = 60.954 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 95 PIXEL DECTRIS PILATUS 2M-F 2018-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.33 50 99.9 0.075 25.2 5 56837
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 1.33 1.35 100 0.784 1.5 4.9
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 1UBQ 1.33 20 53746 3010 99.91 0.137 0.135 0.1349 0.174 0.1735 RANDOM 22.735
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] 0.51 0.23 -0.4 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_sphericity_free 24.228 r_dihedral_angle_4_deg 23.449 r_sphericity_bonded 15.065 r_dihedral_angle_3_deg 11.267 r_dihedral_angle_1_deg 6.345 r_scangle_other 5.664 r_long_range_B_refined 5.138 r_scbond_it 5.025 r_scbond_other 5.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.867 r_sphericity_free 24.228 r_dihedral_angle_4_deg 23.449 r_sphericity_bonded 15.065 r_dihedral_angle_3_deg 11.267 r_dihedral_angle_1_deg 6.345 r_scangle_other 5.664 r_long_range_B_refined 5.138 r_scbond_it 5.025 r_scbond_other 5.023 r_long_range_B_other 4.988 r_rigid_bond_restr 4.556 r_mcangle_it 2.758 r_mcangle_other 2.757 r_mcbond_other 2.265 r_mcbond_it 2.264 r_angle_refined_deg 1.742 r_angle_other_deg 1.047 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1803 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing