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E3 RING ligase binding domain with peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.7 297 23% PEG 6K, 0.1 M NaCl, 50mM HEPES pH 6.7
Crystal Properties Matthews coefficient Solvent content 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.119 α = 90 b = 108.119 β = 90 c = 137.142 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 OXFORD TITAN CCD 2015-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.987 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.17 93.64 99.7 0.103 0.997 12.6 6.4 47982
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.29 0.963
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 2IWG 2.17 93.63 44910 2346 98.49 0.2095 0.2076 0.2141 0.2475 0.2513 RANDOM 40.283
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] 0.41 0.2 0.41 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.678 r_dihedral_angle_4_deg 13.349 r_dihedral_angle_3_deg 11.601 r_dihedral_angle_1_deg 7.758 r_angle_refined_deg 1.397 r_angle_other_deg 1.246 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.678 r_dihedral_angle_4_deg 13.349 r_dihedral_angle_3_deg 11.601 r_dihedral_angle_1_deg 7.758 r_angle_refined_deg 1.397 r_angle_other_deg 1.246 r_chiral_restr 0.068 r_bond_refined_d 0.007 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 5611 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADDREF data reduction Aimless data scaling PHASER phasing