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Covalent Ubiquitin-Usp5 Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBI PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG experimental model PDB 2G43 PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG experimental model PDB 2DAK PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG experimental model PDB 2DAG PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 Crystals of the covalent ubiquitin complex of Usp5 were grown at 298 K using the hanging drop method by mixing equal volumes of protein solution (25 mg/ml) and Crystallization Buffer (1.45 M ammonium sulfate, 0.1 M bis-Tris, pH 6.5, 0.2 M sodium acetate, 5% ethyleneglycol and 1 mM dithiothreitol). The crystals were cryoprotected by immersion in Paratone N in paraffin oil 30% (v/v) and placed in liquid nitrogen., VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.22 61.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.295 α = 90 b = 188.845 β = 90 c = 207.86 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2007-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 35 98 0.101 17.1 5.4 66229 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 94.6 0.845 2 5.4
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 PDB ENTRIES 2IBI, 2G43, 2DAK, 2DAG 2.8 34.9 62592 3298 98.05 0.22688 0.22431 0.2291 0.27588 0.2764 RANDOM 73.948
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] -0.35 0.39 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.014 r_dihedral_angle_4_deg 19.923 r_dihedral_angle_3_deg 19.655 r_dihedral_angle_1_deg 5.975 r_scangle_it 2.237 r_angle_refined_deg 1.308 r_scbond_it 1.275 r_mcangle_it 0.898 r_mcbond_it 0.469 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.014 r_dihedral_angle_4_deg 19.923 r_dihedral_angle_3_deg 19.655 r_dihedral_angle_1_deg 5.975 r_scangle_it 2.237 r_angle_refined_deg 1.308 r_scbond_it 1.275 r_mcangle_it 0.898 r_mcbond_it 0.469 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 11759 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling