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Transcription factor FosB/JunD bZIP domain in its oxidized form, type-III crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VPA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1 M NaCl, 50 mM sodium cacodylate pH 6 and 10 mM spermine
Crystal Properties Matthews coefficient Solvent content 3.49 64.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.008 α = 90 b = 98.051 β = 90 c = 50.251 γ = 90
Symmetry Space Group P 21 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 CCD MARMOSAIC 225 mm CCD 2016-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 2.79 44.72 99.9 0.108 0.116 0.043 7.5 7.1 11778 43.31
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 2.79 2.82 100 0.906 0.977 0.363 0.902 2 7.1
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 5VPA 2.79 44.72 1.34 10789 1068 91.05 0.2547 0.2493 0.2524 0.3002 0.3043 55.163
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 12.825 f_angle_d 0.585 f_chiral_restr 0.029 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1958 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 5
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction DENZO data reduction PHASER phasing