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Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b, wild-type
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 VAPOR DIFFUSION, HANGING DROP 4.5 294 NaCl, PEG 6000, Sodium Acetate, temperature 294K, pH 4.5, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.597 α = 90 b = 49.372 β = 90 c = 62.459 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 SBC-3 2005-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97897 APS 19-BM
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 1.36 50 97.2 0.041 7 31496
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 1.36 1.41 92.6 0.496 2.9
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 (All) 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 1.36 38.72 31463 1590 97.285 0.186 0.186 0.1844 0.1844 0.2237 0.2222 RANDOM 12.87
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] -0.154 -0.29 0.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_4_deg 19.345 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 6.767 r_scangle_it 3.187 r_scbond_it 2.116 r_angle_refined_deg 1.872 r_mcangle_it 1.225 r_mcbond_it 0.994 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_4_deg 19.345 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_1_deg 6.767 r_scangle_it 3.187 r_scbond_it 2.116 r_angle_refined_deg 1.872 r_mcangle_it 1.225 r_mcbond_it 0.994 r_nbtor_refined 0.323 r_symmetry_vdw_refined 0.256 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.124 r_bond_refined_d 0.017 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1187 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction