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Crystal structure of the C-terminal lobe of the human UBR5 HECT domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1M Bis-Tris, 0.2M NaCl, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.84 33.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.24 α = 90.04 b = 39.07 β = 84.59 c = 44.17 γ = 81.77
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 ADSC QUANTUM 210 2010-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE A1 CHESS A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.97 50 90.76 12853 11665 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.97 2.01 93.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 1c4z 1.97 23.11 1 12853 11665 627 90.76 0.22209 0.2192 0.2182 0.27619 0.2757 RANDOM 21.736
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] -0.04 -0.06 0.12 0.11 0.05 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.587 r_dihedral_angle_3_deg 18.11 r_dihedral_angle_4_deg 17.614 r_dihedral_angle_1_deg 5.444 r_scangle_it 2.173 r_scbond_it 1.414 r_angle_refined_deg 1.296 r_mcangle_it 0.86 r_mcbond_it 0.514 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.587 r_dihedral_angle_3_deg 18.11 r_dihedral_angle_4_deg 17.614 r_dihedral_angle_1_deg 5.444 r_scangle_it 2.173 r_scbond_it 1.414 r_angle_refined_deg 1.296 r_mcangle_it 0.86 r_mcbond_it 0.514 r_nbtor_refined 0.3 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.19 r_symmetry_vdw_refined 0.168 r_xyhbond_nbd_refined 0.135 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1502 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling