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Crystal structure of human USP2 C276S mutant in complex with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HD5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 21% PEG3350, 8% Tacsimate (pH8.0)
Crystal Properties Matthews coefficient Solvent content 1.98 37.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.473 α = 90 b = 54.011 β = 107.79 c = 74.753 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 2015-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13C1 0.976 NSRRC BL13C1
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 1.24 30 98.5 0.034 33 3.6 102971
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 1.24 1.28 96.9 0.241 3.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2HD5 1.24 30 102800 5587 98.44 0.14784 0.14694 0.1535 0.16403 0.1688 RANDOM 15.025
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] -0.64 0.18 0.31 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.229 r_sphericity_free 20.77 r_dihedral_angle_4_deg 16.265 r_dihedral_angle_3_deg 11.958 r_dihedral_angle_1_deg 6.019 r_sphericity_bonded 5.003 r_long_range_B_refined 2.003 r_long_range_B_other 1.665 r_angle_refined_deg 1.246 r_rigid_bond_restr 1.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.229 r_sphericity_free 20.77 r_dihedral_angle_4_deg 16.265 r_dihedral_angle_3_deg 11.958 r_dihedral_angle_1_deg 6.019 r_sphericity_bonded 5.003 r_long_range_B_refined 2.003 r_long_range_B_other 1.665 r_angle_refined_deg 1.246 r_rigid_bond_restr 1.173 r_scangle_other 1.135 r_mcangle_it 1.013 r_mcangle_other 1.013 r_scbond_it 0.927 r_scbond_other 0.927 r_angle_other_deg 0.877 r_mcbond_it 0.77 r_mcbond_other 0.769 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3284 Nucleic Acid Atoms Solvent Atoms 356 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data processing PHASER model building HKL-2000 data reduction PHASER phasing HKL-2000 data scaling