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Crystal structure of E3 ligase in complex with peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 16% Jeffamine M-600 pH 7.0 and 0.1 M HEPES 7.0
Crystal Properties Matthews coefficient Solvent content 2.81 56.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.133 α = 90 b = 100.133 β = 90 c = 287.48 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 16M 2019-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
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 2.46 50 99.5 0.059 0.064 0.024 9.1 6.8 53959
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 2.46 2.5 99.9 0.97 1.051 0.397 0.852 6.7
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 5MA4 2.46 47.33 52135 1784 99.56 0.2218 0.2204 0.222 0.2603 0.2622 RANDOM 66.136
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] 1.18 1.18 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.216 r_dihedral_angle_4_deg 17.82 r_dihedral_angle_3_deg 15.934 r_dihedral_angle_1_deg 6.467 r_angle_refined_deg 1.249 r_angle_other_deg 1.227 r_chiral_restr 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.216 r_dihedral_angle_4_deg 17.82 r_dihedral_angle_3_deg 15.934 r_dihedral_angle_1_deg 6.467 r_angle_refined_deg 1.249 r_angle_other_deg 1.227 r_chiral_restr 0.05 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8448 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 5
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction