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Crystal structure of OTUB1 in complex with ubiquitin variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZFY 2zfy, 1ubq experimental model PDB 1UBQ 2zfy, 1ubq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, and 20% (w/v) PEG8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.61 52.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.444 α = 90 b = 109.069 β = 90 c = 73.238 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 6M 2012-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9795 APS 24-ID-E
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 2.5 50 13269 12681 2.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.59 2.69
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2zfy, 1ubq 2.488 46.222 1.37 12681 12212 580 91.52 0.2218 0.2197 0.2184 0.2663 0.2642 RANDOM
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] 2.9516 -2.2483 -0.7033
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.329 f_angle_d 0.715 f_chiral_restr 0.053 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2395 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling