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Crystal structure of 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 8.0 70 MM AMMONIUM SULFATE 17 % PEGMME 5000
Crystal Properties Matthews coefficient Solvent content 3 58.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.256 α = 90 b = 68.153 β = 90 c = 78.262 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 CCD ADSC CCD TOROIDAL MIRROR 2003-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.8 50 100 0.08 0.072 17.8 7.1 19623 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 100 0.59 0.548 3.3 7.3
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FZY 1.8 51.3 18616 997 100 0.169 0.167 0.22 RANDOM 24.61
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] -0.16 -0.04 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.675 r_dihedral_angle_4_deg 21.513 r_dihedral_angle_3_deg 13.474 r_dihedral_angle_1_deg 6.235 r_scangle_it 3.838 r_scbond_it 2.645 r_angle_refined_deg 1.582 r_mcangle_it 1.416 r_mcbond_it 1.292 r_angle_other_deg 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.675 r_dihedral_angle_4_deg 21.513 r_dihedral_angle_3_deg 13.474 r_dihedral_angle_1_deg 6.235 r_scangle_it 3.838 r_scbond_it 2.645 r_angle_refined_deg 1.582 r_mcangle_it 1.416 r_mcbond_it 1.292 r_angle_other_deg 0.9 r_nbd_refined 0.231 r_nbd_other 0.196 r_symmetry_vdw_other 0.184 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.173 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.133 r_chiral_restr 0.115 r_nbtor_other 0.083 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_mcbond_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 1239 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing