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Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 6 {2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethanol}
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JLN PDB entry 4JLN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 285 1.5 M trisodium citrate dehydrate and 25 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.17 43.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.665 α = 90 b = 68.665 β = 90 c = 120.36 γ = 90
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 300 mm CCD 2013-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9785 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 30 99.3 0.044 20.64 43643 43643
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 2.01 98.4 2.54 62.9 6955
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB entry 4JLN 1.9 27.56 41387 41387 2224 99.23 0.2051 0.2051 0.20261 0.2075 0.2501 0.244 RANDOM 40.208
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] 0.14 0.14 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.348 r_dihedral_angle_4_deg 18.741 r_dihedral_angle_3_deg 17.857 r_dihedral_angle_1_deg 6.728 r_long_range_B_refined 2.395 r_long_range_B_other 2.378 r_scangle_other 1.889 r_mcangle_it 1.718 r_mcangle_other 1.717 r_angle_refined_deg 1.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.348 r_dihedral_angle_4_deg 18.741 r_dihedral_angle_3_deg 17.857 r_dihedral_angle_1_deg 6.728 r_long_range_B_refined 2.395 r_long_range_B_other 2.378 r_scangle_other 1.889 r_mcangle_it 1.718 r_mcangle_other 1.717 r_angle_refined_deg 1.649 r_scbond_it 1.533 r_scbond_other 1.533 r_mcbond_it 1.522 r_mcbond_other 1.521 r_angle_other_deg 0.957 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3784 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 110
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling