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Human Ubiquitin-Conjugating Enzyme (E2) UbcH5b mutant Ser94Gly
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 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.514 α = 90 b = 49.295 β = 90 c = 62.617 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 0.97881 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 1.44 50 98.7 0.053 34.2 6.7 26980
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 1.44 1.49 0.544 2.5 3.7
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 1.44 38.72 25571 1369 98.72 0.17495 0.17334 0.1732 0.2047 0.204 RANDOM 22.04
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] -0.82 -0.28 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.218 r_dihedral_angle_1_deg 14.058 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_4_deg 11.898 r_scangle_it 5.039 r_scbond_it 3.379 r_angle_refined_deg 2.369 r_mcangle_it 2.051 r_mcbond_it 1.568 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.218 r_dihedral_angle_1_deg 14.058 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_4_deg 11.898 r_scangle_it 5.039 r_scbond_it 3.379 r_angle_refined_deg 2.369 r_mcangle_it 2.051 r_mcbond_it 1.568 r_nbtor_refined 0.324 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.224 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.154 r_bond_refined_d 0.029 r_gen_planes_refined 0.014 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 1185 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction