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Crystal structure of PopP2 in complex with IP6, AcCoA and the WRKY domain of RRS1-R .
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W3T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 25 mM Tris-HCl (pH 7.5), 250 mM NaCl, 50 mM Arg/Glu, 5% glycerol and 2 mM IP6
Crystal Properties Matthews coefficient Solvent content 3.53 65.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.539 α = 71.54 b = 87.542 β = 84.04 c = 87.548 γ = 84
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 ADSC QUANTUM 315 2016-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
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 1.91 82.81 91.8 0.077 11.4 2.7 80778
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 1.91 1.94 63.7 1.641 0.5 1.5
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 5W3T 2 82.809 1.97 80778 1781 93.97 0.1837 0.1831 0.188 0.2118 0.214
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 14.675 f_angle_d 1.25 f_chiral_restr 0.055 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6270 Nucleic Acid Atoms Solvent Atoms 509 Heterogen Atoms 142
Software Software Software Name Purpose PHENIX refinement Coot model building XDS data scaling PHASER phasing