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Crystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C1T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M MES, 0.1M calcium acetate, 12% PEG8000
Crystal Properties Matthews coefficient Solvent content 1.79 31.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.61 α = 106.09 b = 63.54 β = 107.72 c = 80.91 γ = 90.5
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 2M 2014-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
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 2.5 30.37 90.5 0.05 0.07 0.05 0.995 5.9 1.6 29881 29.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 91 0.163 0.956 1.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2C1T 2.5 27.028 1.97 29866 1542 90.51 0.2152 0.2135 0.2162 0.2466 0.2465
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 14.002 f_angle_d 0.822 f_chiral_restr 0.028 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6667 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction iMOSFLM data reduction