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Crystal structure of the PI5P4Kbeta T201M-2a-ATP complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.1 293 9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M lithium acetate
Crystal Properties Matthews coefficient Solvent content 3 59.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.487 α = 90 b = 184.854 β = 90 c = 106.735 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS EIGER X 16M 2019-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 3.05 47.97 99.9 0.07 24.15 8.8 21000 95.96
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 3.05 3.21 100 0.909 8.6
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 6K4H 3.05 46.22 1.36 20989 1048 99.9 0.2124 0.2092 0.2203 0.2747 0.2819 101.18
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 6.5175 f_angle_d 1.1961 f_chiral_restr 0.0729 f_bond_d 0.0098 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4605 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling Coot model building MOLREP phasing