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Re-interpretation of ppGpp (G4P) electron density in the deposited crystal structure of Xanthine phosphoribosyltransferase (XPRT) (1Y0B).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 100 BIS-TRIS, NaCl, PEG3350, PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.503 α = 90 b = 115.902 β = 94.3 c = 73.985 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 2 1 x-ray 198 CCD CUSTOM-MADE 2003-02-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 2 SYNCHROTRON APS BEAMLINE 19-ID 0.9798 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.8 34.23 88.5 1 58401 19.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 49.7 0.1 0.1 1 0.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MAD FREE R-VALUE 1.8 34.23 1.2 58401 2904 88.45 0.1621 0.1598 0.2083 0.2289 24.69
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 20.0458 f_angle_d 0.8959 f_chiral_restr 0.0567 f_bond_d 0.0054 f_plane_restr 0.0035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5811 Nucleic Acid Atoms Solvent Atoms 749 Heterogen Atoms 152
Software Software Software Name Purpose d*TREK data reduction HKL-2000 data scaling SOLVE phasing SHARP phasing PHENIX refinement