☰ Navigation Tabs
Hexagonal structure of the LDH domain of Human Ubiquitin-conjugating Enzyme E2-like Isoform A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I10 PDB ENTRY 1I10
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 290.9 1.6 M Sodium/potassium phosphate pH 6.5, 0.2 M Sodium chloride, 0.002 M Dithiothreitol, VAPOR DIFFUSION, HANGING DROP, temperature 290.9K
Crystal Properties Matthews coefficient Solvent content 3.23 61.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.603 α = 90 b = 105.603 β = 90 c = 131.918 γ = 120
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 MAR CCD 165 mm 2006-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-BM APS 17-BM
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 2.1 28 100 0.08 28.929 9.2 47978 -3
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) 2.1 2.18 100 0.735 3.32 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 1I10 2.1 27.97 47978 45317 2402 98.88 0.1962 0.19463 0.1956 0.2255 0.2264 RANDOM 27.702
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] 1.48 0.74 1.48 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.869 r_dihedral_angle_4_deg 20.368 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 4.914 r_scangle_it 1.892 r_scbond_it 1.143 r_angle_refined_deg 1.006 r_mcangle_it 0.68 r_mcbond_it 0.348 r_nbtor_refined 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.869 r_dihedral_angle_4_deg 20.368 r_dihedral_angle_3_deg 13.147 r_dihedral_angle_1_deg 4.914 r_scangle_it 1.892 r_scbond_it 1.143 r_angle_refined_deg 1.006 r_mcangle_it 0.68 r_mcbond_it 0.348 r_nbtor_refined 0.287 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.135 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 4354 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 17
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling