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Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CMM PDB ENTRY 3CMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1M Sodium Cacodylate, 0.2M Calcium Acetate, 11.5% Peg8000, 3% 1,5 diaminopentane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.5 α = 90 b = 113.3 β = 90 c = 126.6 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 108 CCD ADSC QUANTUM 315 2012-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979 APS 24-ID-E
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 1 2.9 50 95.2 0.113 8.1 3.4 57810 55035
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 2.9 3 89.4 0.397 2.4 5094
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3CMM 2.9 50 58242 55008 2770 94.4 0.2392 0.2392 0.2392 0.2396 0.2829 0.2815 Random 61.8011
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] -4.782 1.663 3.119
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.537 c_mcangle_it 2.052 c_scbond_it 1.548 c_mcbond_it 1.155 c_angle_d 0.966 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16623 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 76
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection PHASER phasing