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Crystal structure of the ubiquitin conjugating enzyme Ube2g2 bound to the G2BR domain of ubiquitin ligase gp78
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CYX PDB ENTRY 2CYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.7 2.8M SODIUM FORMATE, 0.1M TRIS PH 7.7, 5MM DTT, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 4.84 74.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.719 α = 90 b = 105.719 β = 90 c = 142.855 γ = 90
Symmetry Space Group P 43 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 100 CCD MARMOSAIC 325 mm CCD 2007-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.76 50 99.5 0.105 19.4 8.4 21654 -3 53.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.76 2.86 95.5 0.65 2.1 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB ENTRY 2CYX 2.76 50 20376 2034 94.9 0.216 0.216 0.2162 0.256 0.2555 RANDOM 61.28
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 c_dihedral_angle_d 23.61 c_angle_deg 1.34 c_improper_angle_d 0.98 c_bond_d 0.008 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.61 c_angle_deg 1.34 c_improper_angle_d 0.98 c_bond_d 0.008 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 c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2822 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms
Software Software Software Name Purpose PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling