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Crystal structure of ubiquitin-conjugating enzyme E2-25kDa (Huntington interacting protein 2) M172A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEP PDB entry 2BEP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 Calcium acetate, Sodium acetate, NaCl, PEG 8000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.49 α = 90 b = 134.49 β = 90 c = 38.404 γ = 90
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 MARMOSAIC 300 mm CCD 2008-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.86 50 93.4 0.081 4 27414 2 26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.86 1.91 52.4 0.374 1.98 1.4 1674
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2BEP 1.86 32.38 27404 1403 93.87 0.174 0.172 0.21 0.229 RANDOM 36.498
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.906 r_dihedral_angle_4_deg 16.114 r_dihedral_angle_3_deg 12.945 r_dihedral_angle_1_deg 5.429 r_scangle_it 5.299 r_scbond_it 3.253 r_mcangle_it 2.099 r_angle_refined_deg 1.514 r_mcbond_it 1.361 r_angle_other_deg 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.906 r_dihedral_angle_4_deg 16.114 r_dihedral_angle_3_deg 12.945 r_dihedral_angle_1_deg 5.429 r_scangle_it 5.299 r_scbond_it 3.253 r_mcangle_it 2.099 r_angle_refined_deg 1.514 r_mcbond_it 1.361 r_angle_other_deg 0.939 r_symmetry_vdw_refined 0.32 r_metal_ion_refined 0.258 r_mcbond_other 0.252 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.208 r_nbd_other 0.201 r_symmetry_vdw_other 0.186 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.095 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1597 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 1
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction SCALEPACK data scaling