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Structure of the SAGA Ubp8(S144N)/Sgf11(1-72, Delta-ZnF)/Sus1/Sgf73 DUB module
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MHS PDB entry 3MHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 14% PEG3350, 0.18-0.22 M Tri-ammonium citrate, 8-14% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.973 α = 90 b = 79.975 β = 90 c = 274.259 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 108 CCD MARMOSAIC 300 mm CCD 2010-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 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 2.686 50 91.9 0.151 0.151 12.227 7.8 47615 43495 -3
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 2.686 2.74 84.9 0.637 0.637 2.345 6.2
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 (All) 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 3MHS 2.686 47.18 47615 41136 2192 90.97 0.18717 0.18717 0.18329 0.188 0.26361 0.269 RANDOM 44.481
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] 3.15 -0.2 -2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.891 r_dihedral_angle_3_deg 18.25 r_dihedral_angle_4_deg 14.528 r_dihedral_angle_1_deg 6.633 r_angle_refined_deg 1.545 r_angle_other_deg 0.963 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.891 r_dihedral_angle_3_deg 18.25 r_dihedral_angle_4_deg 14.528 r_dihedral_angle_1_deg 6.633 r_angle_refined_deg 1.545 r_angle_other_deg 0.963 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10616 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 14
Software Software Software Name Purpose Locally data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling