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Crystal structure of E3 ligase
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 2.52 51.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.003 α = 90 b = 97.003 β = 90 c = 148.341 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 PIXEL DECTRIS PILATUS3 6M 2019-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97890 APS 24-ID-C
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 2.03 50 97.6 0.068 0.075 0.032 11 5.2 99464 38.36
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 2.03 2.07 82.1 0.836 0.95 0.441 0.599 3.6
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 2.03 49.45 98614 4820 97.8 0.219 0.218 0.2273 0.242 0.2565 RANDOM 48.96
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] 3.3206 3.3206 -6.6411
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.65 t_omega_torsion 2.47 t_angle_deg 1.02 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.65 t_omega_torsion 2.47 t_angle_deg 1.02 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10456 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose SCALEPACK data scaling BUSTER refinement PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing