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Crystal structure of human adenosine kinase (ADK) in complex with inhibitor BKI-1817
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 291 2.4M ammonium sulfate, 0.1M Citrate pH 4.0. HosaA.19365.a.VZ21.PC00201 at 18 mg/mL. Cocrystallization with 2mM inhibitor. plate 14484 A12 drop 2, Puck: PSL1601, Cryo: 2.5M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 3.49 64.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.635 α = 90 b = 112.635 β = 90 c = 115.121 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS EIGER2 XE 9M 2024-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
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 2.51 46.65 100 0.16 0.163 0.032 0.999 20.3 25.9 25975
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 2.51 2.58 99.9 2.859 2.915 0.565 0.499 26.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.51 46.65 1.34 25913 1247 99.94 0.2159 0.2143 0.2172 0.2457 0.2507
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 21.159 f_angle_d 0.541 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2655 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 107
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction