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High-resolution crystal structure of the UBC core domain of UBE2E1/UbcH6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.1M Sodium citrate pH 6 and 8% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.1 39.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.301 α = 90 b = 40.555 β = 90 c = 91.317 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.282416 BESSY 14.1
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 1.42 37.06 94.8 0.049 0.999 33.21 11.568 26209
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 1.42 1.51 79.2 0.113 13.15 9.66
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.42 37.06 26190 1311 94.72 0.1558 0.1543 0.154 0.183 0.1828 RANDOM 17.7812
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] 0.05 -0.32 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.462 r_dihedral_angle_4_deg 17.543 r_dihedral_angle_3_deg 11.563 r_dihedral_angle_1_deg 5.683 r_angle_other_deg 3.644 r_angle_refined_deg 2.134 r_mcangle_it 1.529 r_mcbond_it 0.96 r_mcbond_other 0.925 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.462 r_dihedral_angle_4_deg 17.543 r_dihedral_angle_3_deg 11.563 r_dihedral_angle_1_deg 5.683 r_angle_other_deg 3.644 r_angle_refined_deg 2.134 r_mcangle_it 1.529 r_mcbond_it 0.96 r_mcbond_other 0.925 r_chiral_restr 0.137 r_bond_refined_d 0.022 r_gen_planes_other 0.022 r_gen_planes_refined 0.013 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1212 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction REFMAC refinement XDS data reduction XDS data scaling PHASER phasing