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Transcription factor FosB/JunD bZIP domain covalently modified with the cysteine-targeting alpha-haloketone compound Z2159931480
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VPF 5VPF, poly-alanine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 100 mM Tris HCl pH 7.0, 40% (v/v) Ethanol
Crystal Properties Matthews coefficient Solvent content 3.28 62.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.26 α = 90 b = 67.67 β = 90 c = 122.943 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 X 9M 2021-04-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.446 44.923 84.9 0.216 0.233 0.085 0.996 6.7 7.2 3060
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 2.446 2.779 72.7 2.605 2.804 1.019 0.664 1.3 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5VPF, poly-alanine 3.21 35.05 1.33 2514 191 71.24 0.2845 0.2804 0.2853 0.3297 0.3322 40.65
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 5.2757 f_angle_d 1.0904 f_chiral_restr 0.0417 f_bond_d 0.0087 f_plane_restr 0.0077
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1017 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PDB_EXTRACT data extraction PHASER phasing Coot model building