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Structure of yeast SAGA DUBm with Sgf73 Y57A mutant at 2.8 angstroms resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MHS
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 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.739 α = 90 b = 67.273 β = 106.84 c = 137.145 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 2013-05-18 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 2.8 47.02 99.8 23.2 3.8 34989
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 3MHS 2.8 47.02 33234 1755 99.7 0.18496 0.182 0.1841 0.24067 0.2366 RANDOM 51.258
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] -1.35 2.64 -3.58 3.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 17.531 r_dihedral_angle_3_deg 16.87 r_dihedral_angle_1_deg 6.029 r_angle_refined_deg 1.371 r_angle_other_deg 0.93 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.202 r_dihedral_angle_4_deg 17.531 r_dihedral_angle_3_deg 16.87 r_dihedral_angle_1_deg 6.029 r_angle_refined_deg 1.371 r_angle_other_deg 0.93 r_chiral_restr 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.003 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 10484 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection Coot model building HKL-2000 data scaling PHENIX refinement