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Structure of C. elegans OTUB1 bound to human UBC13
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J7D PDB ENTRIES 1J7D and 2ZFY experimental model PDB 2ZFY PDB ENTRIES 1J7D and 2ZFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 100 mM sodium cacodylate, 1 M trisodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.23 61.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.07 α = 90 b = 111.07 β = 90 c = 179.612 γ = 120
Symmetry Space Group P 61 2 2
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 2010-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.034 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 41 99.9 61151 61151 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1J7D and 2ZFY 1.8 40.72 61151 57931 3084 99.82 0.18782 0.18673 0.1886 0.20866 0.2123 RANDOM 29.876
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] 0.36 0.18 0.36 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.288 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 14.484 r_dihedral_angle_1_deg 5.251 r_scangle_it 4.166 r_scbond_it 2.43 r_mcangle_it 1.764 r_angle_refined_deg 1.249 r_mcbond_it 0.907 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.288 r_dihedral_angle_4_deg 16.998 r_dihedral_angle_3_deg 14.484 r_dihedral_angle_1_deg 5.251 r_scangle_it 4.166 r_scbond_it 2.43 r_mcangle_it 1.764 r_angle_refined_deg 1.249 r_mcbond_it 0.907 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 3115 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms
Software Software Software Name Purpose iMOSFLM data reduction REFMAC refinement SCALA data scaling PHASER phasing