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Crystal Structure of S. Cerevisiae SUMO E3 Ligase SIZ2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 20 mM Tris-HCl pH8
100 mM NaCl
20% glycerol
1 mM beta-mercaptoethanol
40 % PEG3350
Crystal Properties Matthews coefficient Solvent content 3.16 61.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.916 α = 90 b = 80.689 β = 94.995 c = 76.527 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 PIXEL DECTRIS PILATUS 6M-F 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.63 49 94.5 0.09 0.107 0.057 0.995 11.15 3.1 21200 44.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.63 2.73 86.9 0.483 0.581 0.316 0.726 1.69 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3I2D 2.63 49 1.42 21188 1060 94.54 0.2201 0.2178 0.2627 0.256 48.42
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.988 f_angle_d 0.4826 f_chiral_restr 0.0409 f_plane_restr 0.0028 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4196 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing