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Transition state analogue(GMPK in complex with GMP, ADP, Mg2+ and AlF4- at 293 K)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9JAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 40% PEG4000, 0.1 M ammonium acetate, 0.1 M trisodium citrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.685 α = 90 b = 96.685 β = 90 c = 45.338 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER2 S 9M 2024-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.979183 SSRF BL02U1
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 1.8 48.34 99.9 0.039 0.043 0.017 1 27.1 5.8 22625
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 1.8 1.84 100 0.259 0.285 0.117 0.947 5.8
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 9JAI 1.8 33.07 1.37 22610 1133 99.91 0.1727 0.1711 0.1708 0.2032 0.203
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 18.303 f_angle_d 0.932 f_chiral_restr 0.052 f_plane_restr 0.008 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1506 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 57
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction MOLREP phasing