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USP7 in complex with macrocycle MC09
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, HANGING DROP 7 293 25% w/v PEG 1500 and 0.1 M MMT (malic acid, MES, Tris) buffer pH 7
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 244.997 α = 90 b = 68.848 β = 105.21 c = 76.052 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 100 PIXEL DECTRIS PILATUS3 6M 2022-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00004 ALS 5.0.2
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 2.57 73.39 69.2 0.048 0.058 0.04 0.999 9.7 3.4 27109 68.19
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 2.572 2.664 5.32 0.743 0.869 0.61 0.582 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.57 73.39 1.34 27101 1370 69.21 0.2488 0.2469 0.2487 0.2841 0.283 74.74
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 f_dihedral_angle_d 16.3704 f_angle_d 0.579 f_chiral_restr 0.0407 f_plane_restr 0.0041 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7984 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing