☰ Navigation Tabs
Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin (malonate bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NB8 1NB8, 1UBQ experimental model PDB 1UBQ 1NB8, 1UBQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 292 8% tacsimate pH 4.0, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.08 40.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.33 α = 90 b = 43.54 β = 107.55 c = 84.76 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 CCD ADSC QUANTUM 315r 2016-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.98 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.426 40.53 99.5 0.073 0.994 8.3 3 75388 14.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.43 1.45 99.2 0.384 0.799 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1NB8, 1UBQ 1.426 40.529 1.35 75376 2000 99.5 0.1707 0.1701 0.1916 0.2139 21.2826
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 16.359 f_angle_d 0.966 f_chiral_restr 0.078 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3364 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction