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Crystal structure of the CUE domain of the E3 ubiquitin ligase AMFR (gp78)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 0.056 M sodium phosphate, 1.344 M potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.396 α = 90 b = 55.396 β = 90 c = 30.993 γ = 120
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 2012-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9183 CHESS F1
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 1.6 50 0.9996 0.075 55.2 11.1 6932 6929 1 1
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 1.6 1.63 100 0.44 8.1 11 503
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 (All) 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 2ejs 1.6 48 1 6932 6929 339 99.96 0.161 0.16001 0.15872 0.1634 0.18626 0.1943 RANDOM 23.977
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] -0.43 -0.21 -0.43 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.197 r_dihedral_angle_3_deg 15.903 r_dihedral_angle_4_deg 15.325 r_dihedral_angle_1_deg 3.72 r_scangle_it 2.971 r_scbond_it 1.837 r_angle_refined_deg 1.09 r_mcangle_it 1.035 r_mcbond_it 0.662 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.197 r_dihedral_angle_3_deg 15.903 r_dihedral_angle_4_deg 15.325 r_dihedral_angle_1_deg 3.72 r_scangle_it 2.971 r_scbond_it 1.837 r_angle_refined_deg 1.09 r_mcangle_it 1.035 r_mcbond_it 0.662 r_nbtor_refined 0.309 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.127 r_xyhbond_nbd_refined 0.097 r_symmetry_hbond_refined 0.093 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 432 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling