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Crystal structure of covalent ubiquitin-USP21 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBI PDB ENTRY 2IBI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 13% PEG 3350, 0.1 M Bis-Tris, 0.1 M Ammonium sulfate, 5 mM TCEP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.428 α = 88.71 b = 83.663 β = 75.73 c = 118.792 γ = 85.11
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 MARMOSAIC 300 mm CCD 2008-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97949 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.59 83.37 96.3 0.08 0.083 9.81 2.54 65088 65088
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.61 95.6 0.416 0.529 2.08 2.56
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 PDB ENTRY 2IBI 2.59 83.37 61793 3293 95.8 0.18777 0.18614 0.2075 0.21801 0.2367 RANDOM 43.685
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] -14.9 5.35 4.35 13.28 -24 1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.513 r_dihedral_angle_4_deg 22.749 r_dihedral_angle_3_deg 22.173 r_dihedral_angle_1_deg 7.466 r_scangle_it 4.852 r_scbond_it 2.857 r_angle_refined_deg 1.998 r_mcangle_it 1.9 r_mcbond_it 0.978 r_chiral_restr 0.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.513 r_dihedral_angle_4_deg 22.749 r_dihedral_angle_3_deg 22.173 r_dihedral_angle_1_deg 7.466 r_scangle_it 4.852 r_scbond_it 2.857 r_angle_refined_deg 1.998 r_mcangle_it 1.9 r_mcbond_it 0.978 r_chiral_restr 0.131 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12293 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 16
Software Software Software Name Purpose CBASS data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling