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Crystal structure of human UBC4 E2 conjugating enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X23 PDB ENTRY 1X23
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 2M sodium formate, 0.1M sodium acetate trihydrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 28.23 α = 90 b = 59.12 β = 106.73 c = 45.24 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.54
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 1.6 43.31 99.92 0.061 17.14 3.7 17905
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) 1.6 1.64 99.5 0.123 13.15 3.6
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1X23 1.6 43.31 17905 958 99.93 0.18918 0.187 0.2006 0.229 0.2399 RANDOM 6.751
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 0.21 0.03 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.328 r_dihedral_angle_4_deg 18.879 r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 6.263 r_scangle_it 4.907 r_scbond_it 3.287 r_angle_refined_deg 2.018 r_mcangle_it 1.728 r_mcbond_it 0.97 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.328 r_dihedral_angle_4_deg 18.879 r_dihedral_angle_3_deg 12.409 r_dihedral_angle_1_deg 6.263 r_scangle_it 4.907 r_scbond_it 3.287 r_angle_refined_deg 2.018 r_mcangle_it 1.728 r_mcbond_it 0.97 r_chiral_restr 0.135 r_bond_refined_d 0.023 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling