☰ Navigation Tabs
Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E0C PDB entries 3E0C & 2JRS experimental model PDB 2JRS PDB entries 3E0C & 2JRS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.1 M sodium HEPES, pH 7.0, 15% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.507 α = 90 b = 94.767 β = 98.06 c = 145.706 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 X 6M 2018-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.9 50 96.9 0.087 0.102 0.052 6.5 3.6 47114 53.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 92.3 0.487 0.575 0.298 0.818 1.4 3.3
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 entries 3E0C & 2JRS 2.9 49.45 44775 2310 96.26 0.2104 0.2083 0.2083 0.2518 0.2518 RANDOM 86.922
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] -2.65 2.33 -0.71 2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.151 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 15.99 r_dihedral_angle_1_deg 6.894 r_angle_refined_deg 1.126 r_chiral_restr 0.096 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13087 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing