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Human ubiquitin conjugating enzyme E2E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QCQ PDB ENTRY 1QCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 298 2M (NH4)2SO4, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 46.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.109 α = 90 b = 36.11 β = 99.92 c = 130.568 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE RIGAKU RAXIS IV++ MIRRORS 2004-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E
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 1.85 19.26 90.5 0.044 23.28 3.2 39009 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 91.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1QCQ 1.85 20 37014 37014 1995 90.51 0.19449 0.19174 0.1918 0.24595 0.2449 RANDOM 31.993
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] -1.34 0.13 2.13 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_3_deg 15.655 r_dihedral_angle_4_deg 14.507 r_dihedral_angle_1_deg 5.673 r_scangle_it 4.285 r_scbond_it 2.762 r_mcangle_it 1.723 r_angle_refined_deg 1.588 r_mcbond_it 1.058 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.318 r_dihedral_angle_3_deg 15.655 r_dihedral_angle_4_deg 14.507 r_dihedral_angle_1_deg 5.673 r_scangle_it 4.285 r_scbond_it 2.762 r_mcangle_it 1.723 r_angle_refined_deg 1.588 r_mcbond_it 1.058 r_nbtor_refined 0.315 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.185 r_xyhbond_nbd_refined 0.179 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3486 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing