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The Crystal Structure of USP8 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 15% PEG 2000 MME, 0.1M Bis-Tris propane pH6.9
Crystal Properties Matthews coefficient Solvent content 2.2 44.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.83 α = 90 b = 109.342 β = 90 c = 180.992 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2023-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95355 CLSI 08ID-1
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 2.1 48.777 99.5 0.149 11.7 9 67580
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 2.1 2.15 0.973
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 48.777 67509 3285 99.383 0.178 0.1765 0.1851 0.216 0.2232 35.216
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] -0.838 0.379 0.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.274 r_dihedral_angle_other_3_deg 13.09 r_dihedral_angle_3_deg 12.258 r_lrange_it 6.868 r_lrange_other 6.853 r_dihedral_angle_1_deg 6.36 r_dihedral_angle_2_deg 5.046 r_scangle_it 4.912 r_scangle_other 4.912 r_mcangle_it 3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.274 r_dihedral_angle_other_3_deg 13.09 r_dihedral_angle_3_deg 12.258 r_lrange_it 6.868 r_lrange_other 6.853 r_dihedral_angle_1_deg 6.36 r_dihedral_angle_2_deg 5.046 r_scangle_it 4.912 r_scangle_other 4.912 r_mcangle_it 3.78 r_mcangle_other 3.78 r_scbond_it 3.013 r_scbond_other 3.013 r_mcbond_it 2.395 r_mcbond_other 2.393 r_angle_refined_deg 1.25 r_angle_other_deg 0.449 r_nbd_other 0.22 r_nbd_refined 0.206 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.178 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.149 r_symmetry_nbd_refined 0.138 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.066 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8197 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing