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Crystal structure of ZER1 bound to GAGN degron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M Sodium formate, 23% (wt/vol) Polyethylene glycol 3,350, 0.033% (wt/vol) Anthrone, 0.033% (wt/vol) Congo Red, 0.033% (wt/vol) N-(2-Acetamido)-2-aminoethanesulfonic acid, 0.002 M HEPES sodium pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.48 50.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.97 α = 90 b = 120.42 β = 90 c = 68 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD MAR CCD 165 mm 2020-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979191 SSRF BL17U1
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 1.51 59.19 98.8 0.038 30.6 11 43366 23.2
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 1.51 1.55 0.44 2.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7EP0 1.513 22.323 43322 1983 97.94 0.2189 0.2197 0.2555 0.2575 28.5
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.2076 f_angle_d 0.7521 f_chiral_restr 0.0465 f_bond_d 0.0057 f_plane_restr 0.0051
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1964 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing