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CRYSTAL STRUCTURE OF UBIQUITIN K27M MUTANT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 CdCl2 (0.2 M), PEG400 (10% v/v), 2-methyl-2,4-pentanediol (12% v/v) and sodium acetate buffer (0.1 M, pH 4.6)
Crystal Properties Matthews coefficient Solvent content 3.95 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.574 α = 90 b = 144.574 β = 90 c = 144.574 γ = 90
Symmetry Space Group F 4 3 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 EIGER2 XE 9M 2024-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.978570 NSLS-II 19-ID
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 1.5 40 99.6 0.065 0.069 0.022 1 10.9 9.5 21257
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 1.5 1.53 97.7 0.756 0.848 0.374 0.667 5.1
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 SAD THROUGHOUT 1.5 33.19 19817 1064 97.88 0.12979 0.12855 0.1289 0.15367 0.1536 RANDOM 24.001
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.932 r_dihedral_angle_4_deg 24.875 r_dihedral_angle_3_deg 14.735 r_scangle_other 7.676 r_scbond_it 6.688 r_scbond_other 6.678 r_long_range_B_refined 6.554 r_dihedral_angle_1_deg 6.23 r_long_range_B_other 6.218 r_rigid_bond_restr 6.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.932 r_dihedral_angle_4_deg 24.875 r_dihedral_angle_3_deg 14.735 r_scangle_other 7.676 r_scbond_it 6.688 r_scbond_other 6.678 r_long_range_B_refined 6.554 r_dihedral_angle_1_deg 6.23 r_long_range_B_other 6.218 r_rigid_bond_restr 6.039 r_mcangle_other 3.813 r_mcangle_it 3.75 r_mcbond_it 3.091 r_mcbond_other 2.766 r_angle_refined_deg 2.115 r_angle_other_deg 1.574 r_chiral_restr 0.116 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 573 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction AutoSol phasing PDB_EXTRACT data extraction