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Crystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FZY PDB ENTRY 1FZY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 MM TRIS PH 8.5 200 MM MAGNESIUM CHLORIDE 17% PEG 4000 10 % GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.4 48.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.391 α = 90 b = 58.391 β = 90 c = 162.842 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 ADSC ADSC Q4R TOROIDAL MIRROR 2003-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.3 50 99.9 0.07 30.6 13.4 13257 -3
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 2.3 2.42 99.5 0.53 3.8 13
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FZY 2.3 55.05 12545 651 99.6 0.213 0.21 0.2134 0.279 RANDOM 53.66
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] -2.04 -2.04 4.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.697 r_dihedral_angle_4_deg 20.63 r_dihedral_angle_3_deg 17.644 r_dihedral_angle_1_deg 7.276 r_scangle_it 2.496 r_scbond_it 1.755 r_angle_refined_deg 1.64 r_mcangle_it 0.979 r_angle_other_deg 0.927 r_mcbond_it 0.813
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.697 r_dihedral_angle_4_deg 20.63 r_dihedral_angle_3_deg 17.644 r_dihedral_angle_1_deg 7.276 r_scangle_it 2.496 r_scbond_it 1.755 r_angle_refined_deg 1.64 r_mcangle_it 0.979 r_angle_other_deg 0.927 r_mcbond_it 0.813 r_symmetry_hbond_refined 0.319 r_symmetry_vdw_other 0.272 r_nbd_refined 0.198 r_nbd_other 0.19 r_nbtor_refined 0.183 r_mcbond_other 0.173 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.095 r_nbtor_other 0.089 r_symmetry_vdw_refined 0.075 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1853 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing