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Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ile37Ala
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ESK PDB ENTRY 2ESK
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 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.654 α = 90 b = 49.429 β = 90 c = 63.037 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 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 1.5 50 99 0.058 42.6 9.4 24280
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 1.5 1.55 0.796 2.6 5.6
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 2ESK 1.5 38.9 23013 1231 98.89 0.17938 0.17723 0.1764 0.21913 0.2152 RANDOM 22.78
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] 0.34 -0.32 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.205 r_dihedral_angle_1_deg 18.176 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_4_deg 11.524 r_scangle_it 4.066 r_scbond_it 2.762 r_angle_refined_deg 2.067 r_mcangle_it 1.634 r_mcbond_it 1.298 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.205 r_dihedral_angle_1_deg 18.176 r_dihedral_angle_3_deg 14.664 r_dihedral_angle_4_deg 11.524 r_scangle_it 4.066 r_scbond_it 2.762 r_angle_refined_deg 2.067 r_mcangle_it 1.634 r_mcbond_it 1.298 r_nbtor_refined 0.325 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.205 r_symmetry_vdw_refined 0.191 r_chiral_restr 0.169 r_xyhbond_nbd_refined 0.161 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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 1184 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction