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Crystal structure of HCK kinase complexed with a pyrrolo-pyrimidine inhibitor 7-[trans-4-(4-methylpiperazin-1-yl)cyclohexyl]-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HK5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.1 M Tris-HCl (pH 8.5)
25 % (v/v) PEG 10,000
Crystal Properties Matthews coefficient Solvent content 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.81 α = 87.59 b = 48.02 β = 83.09 c = 78.01 γ = 63.59
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 MARMOSAIC 225 mm CCD 2014-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.696 38.094 92.1 0.06 0.085 0.995 8.4 1.989 56349
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.8 90 0.452 0.638 0.725 1.67 1.954
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 THROUGHOUT 2HK5 1.696 38.094 1.98 56327 2005 92.04 0.2078 0.2066 0.2088 0.2401 0.2403 21.5299
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 11.796 f_angle_d 0.656 f_chiral_restr 0.047 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4353 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms 72
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction