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Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 100mM Bis Tris, 18% PEG3350, 100mM Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.09 41.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.076 α = 90 b = 68.004 β = 106.75 c = 137.858 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 300 mm CCD 2013-06-28 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 2.36 47.41 100 23 3.8 59279
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.36 47.41 56297 2993 99.8 0.18615 0.18307 0.192 0.2438 0.2492 RANDOM 36.681
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] -0.1 0.89 2.75 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.629 r_dihedral_angle_4_deg 17.831 r_dihedral_angle_3_deg 16.522 r_dihedral_angle_1_deg 6.587 r_angle_refined_deg 1.654 r_angle_other_deg 0.831 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.629 r_dihedral_angle_4_deg 17.831 r_dihedral_angle_3_deg 16.522 r_dihedral_angle_1_deg 6.587 r_angle_refined_deg 1.654 r_angle_other_deg 0.831 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10935 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection Coot model building HKL-2000 data scaling PHENIX refinement