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Human ubiquitin-conjugating enzyme (E2) UbcH5b mutant Ile88Ala
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 = 47.877 α = 90 b = 49.224 β = 90 c = 62.128 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 1.52 50 98.7 0.045 31.6 4.9 22996
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 1.52 1.57 91 0.522 2.2 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 2ESK 1.52 38.58 21765 1168 98.76 0.18663 0.18415 0.1822 0.23342 0.2339 RANDOM 18.722
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] -0.18 -0.35 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.036 r_dihedral_angle_4_deg 17.492 r_dihedral_angle_1_deg 13.488 r_dihedral_angle_3_deg 13.101 r_scangle_it 4.035 r_scbond_it 2.662 r_angle_refined_deg 2.084 r_mcangle_it 1.595 r_mcbond_it 1.182 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.036 r_dihedral_angle_4_deg 17.492 r_dihedral_angle_1_deg 13.488 r_dihedral_angle_3_deg 13.101 r_scangle_it 4.035 r_scbond_it 2.662 r_angle_refined_deg 2.084 r_mcangle_it 1.595 r_mcbond_it 1.182 r_nbtor_refined 0.326 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.169 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.138 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 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 136 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction