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Co-crystal structure of znf ubp domain from the deubiquitinating enzyme isopeptidase T (isot) in complex with ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G43 PDB ENTRY 2G43
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 300 16% polyethylene glycol 8000, 80 mM sodium cacodylate pH 6.5, 160 mM magenesium or calcium acetate, 20% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 300K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 3.25 62.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.074 α = 90 b = 68.074 β = 90 c = 225.345 γ = 120
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 MARRESEARCH 2005-07-09 M SINGLE WAVELENGTH 2 1 x-ray M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0, 1.28317, 1.27163, 1.28855, 1.28237 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2,1 1.99 35 99.9 0.087 13.9 10.4 40453 -3 23.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.99 2.06 100 0.367 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2G43 1.99 35 40453 39760 3990 98.5 0.229 0.229 0.268 RANDOM 41.8
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] 5.52 1.93 5.52 -11.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 2.89 c_mcangle_it 2.02 c_scbond_it 1.88 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.74 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.6 c_scangle_it 2.89 c_mcangle_it 2.02 c_scbond_it 1.88 c_angle_deg 1.3 c_mcbond_it 1.26 c_improper_angle_d 0.74 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3034 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 3
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling SOLVE phasing CNS refinement HKL-2000 data reduction