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DYRK1A Kinase Domain in Complex with a 6-azaindole Derivative, GNF2133.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VX3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 15% PEG 20000, 3% Eextran Sulfate, 100 mM Bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 4.45 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.884 α = 90 b = 112.884 β = 90 c = 304.651 γ = 120
Symmetry Space Group P 31 1 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 CCD ADSC QUANTUM 315r 2014-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) 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 3.7 48.26 98.48 0.122 0.048 24.9 8.4 23849 24.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.7 3.83 86.14 0.58 0.865 1.4 8.4
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2VX3 3.7 48.26 1.34 23736 1155 98.54 0.2724 0.2714 0.2723 0.2904 0.2885 Random 48.08
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 5.1355 f_angle_d 0.641 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8107 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing