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The Crystal Structure of human USP7 USP domain from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Tris pH8.5, 25% PEG3,350
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.05 α = 90 b = 69.131 β = 96.076 c = 76.858 γ = 90
Symmetry Space Group P 1 21 1
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 16M 2020-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97918 SSRF BL17U1
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 2.25 19.685 99.7 0.066 12 3.7 37704
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 2.25 2.32 0.66
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1nb8 2.25 19.685 37690 1822 99.593 0.198 0.1963 0.2015 0.236 0.2356 44.569
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] -1.202 1.008 3.45 -2.408
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_4_deg 14.389 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 6.555 r_lrange_it 5.067 r_lrange_other 5.021 r_mcangle_it 3.022 r_mcangle_other 3.021 r_scangle_it 2.752 r_scangle_other 2.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.744 r_dihedral_angle_4_deg 14.389 r_dihedral_angle_3_deg 14.35 r_dihedral_angle_1_deg 6.555 r_lrange_it 5.067 r_lrange_other 5.021 r_mcangle_it 3.022 r_mcangle_other 3.021 r_scangle_it 2.752 r_scangle_other 2.752 r_mcbond_it 1.736 r_mcbond_other 1.736 r_scbond_it 1.589 r_scbond_other 1.588 r_angle_refined_deg 1.177 r_angle_other_deg 1.081 r_nbd_refined 0.173 r_symmetry_nbd_other 0.165 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.131 r_nbd_other 0.124 r_symmetry_nbd_refined 0.114 r_symmetry_nbtor_other 0.07 r_symmetry_xyhbond_nbd_refined 0.067 r_chiral_restr 0.043 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 5499 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing