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Crystal Structure of a threonine-selective RCR E3 ligase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 277 23.3 mM Na2HPO4
23.3 mM (NH4)2SO4
23.3 mM NaNO3
18 % PEG500 MME
9 % PEG20000
Crystal Properties Matthews coefficient Solvent content 3.38 63.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.578 α = 90 b = 82.578 β = 90 c = 103.303 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 PILATUS 6M 2017-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.2823 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.75 40 99.3 0.051 18.3 6.9 40007 18.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 93.3 0.404 2.4 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.75 40 39140 823 99.31 0.17245 0.17192 0.1835 0.1957 0.205 RANDOM 28.7
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] -0.18 -0.09 -0.18 0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.625 r_dihedral_angle_4_deg 19.889 r_dihedral_angle_3_deg 13.666 r_long_range_B_refined 7.355 r_long_range_B_other 7.32 r_dihedral_angle_1_deg 6.447 r_scangle_other 5.898 r_scbond_it 3.862 r_scbond_other 3.862 r_mcangle_other 3.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.625 r_dihedral_angle_4_deg 19.889 r_dihedral_angle_3_deg 13.666 r_long_range_B_refined 7.355 r_long_range_B_other 7.32 r_dihedral_angle_1_deg 6.447 r_scangle_other 5.898 r_scbond_it 3.862 r_scbond_other 3.862 r_mcangle_other 3.312 r_mcangle_it 3.305 r_mcbond_it 2.517 r_mcbond_other 2.506 r_angle_refined_deg 1.962 r_angle_other_deg 0.979 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1980 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling SHELXD phasing