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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 2A9U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 4.0M Na formate
Crystal Properties Matthews coefficient Solvent content 2.84 56.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.008 α = 90 b = 103.008 β = 90 c = 93.254 γ = 120
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 PILATUS3 S 6M 2020-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.239850 CLSI 08B1-1
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 3.1 40.24 98.7 0.119 9.6 5.5 3507
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 3.1 3.31 0.824
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 3.1 40.24 3507 166 97.824 0.201 0.1979 0.2054 0.2681 0.2742 87.712
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] 2.62 1.31 2.62 -8.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.725 r_dihedral_angle_3_deg 12.271 r_lrange_it 9.399 r_lrange_other 9.373 r_scangle_it 5.547 r_scangle_other 5.543 r_dihedral_angle_1_deg 5.519 r_mcangle_it 5.307 r_mcangle_other 5.307 r_mcbond_it 3.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.725 r_dihedral_angle_3_deg 12.271 r_lrange_it 9.399 r_lrange_other 9.373 r_scangle_it 5.547 r_scangle_other 5.543 r_dihedral_angle_1_deg 5.519 r_mcangle_it 5.307 r_mcangle_other 5.307 r_mcbond_it 3.454 r_mcbond_other 3.42 r_dihedral_angle_2_deg 3.381 r_scbond_it 3.351 r_scbond_other 3.345 r_angle_refined_deg 0.749 r_angle_other_deg 0.272 r_nbd_refined 0.226 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.177 r_symmetry_xyhbond_nbd_refined 0.176 r_xyhbond_nbd_refined 0.173 r_nbd_other 0.151 r_symmetry_nbd_refined 0.142 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.036 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1060 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing