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Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4II2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.1 M Tris-HCl pH 8.0-8.5, 0.3-0.4 M lithium sulfate, 15-18% w/v polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.92 57.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.111 α = 102.1 b = 82.238 β = 95.78 c = 135.376 γ = 90.86
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 RAYONIX MX300-HS 2014-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 29.7 96.9 0.051 0.97 10.2 3.5 108289
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 2.55 93.2 0.289 0.34 3.1 3.5
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4II2 2.5 28.314 2.53 108284 10828 96.88 0.2196 0.216 0.2188 0.2513 0.2517 random selection
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 11.994 f_angle_d 0.699 f_chiral_restr 0.027 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19279 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 45
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing