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Crystal structure of Human FN3K bound with ADP and DMF (I)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9CX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 -crystallized in 0.5 M ammonium sulfate, 0.1 M tri-sodium citrate, and 1 M lithium sulfate
-soaked in 10 mM DMF, 5 mM MgSO4 and 2.5 mM ADP-AlF3
-cryo-protected in 0.9X reservoir solution + 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.98 58.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.833 α = 90 b = 112.034 β = 90 c = 132.929 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2021-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92011 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 29.72 99.9 0.056 0.99 18 6.8 73993
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 0.85
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 1.8 29.72 1.34 73910 1999 99.87 0.1776 0.1768 0.1769 0.2047 0.2047
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 13.256 f_angle_d 1.559 f_chiral_restr 0.106 f_bond_d 0.018 f_plane_restr 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4543 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 152
Software Software Software Name Purpose PHENIX refinement Coot model building RAPD data processing PHASER phasing RAPD data reduction RAPD data scaling