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Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 4 [1-[5-(4-{[(2,6-diaminopyrimidin-4-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]-2-methylpropan-2-ol]
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 2.21 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.75 α = 90 b = 68.75 β = 90 c = 122.45 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 2012-11-20 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 2 30 99.4 0.059 13.6 38119 38119
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.1 99.9 0.547 2.75 5189
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 2 27.97 36194 36194 1924 99.38 0.18485 0.18485 0.18308 0.1883 0.21613 0.2175 RANDOM 46.465
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] -2.98 -2.98 5.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.649 r_dihedral_angle_4_deg 17.484 r_dihedral_angle_3_deg 16.813 r_dihedral_angle_1_deg 6.295 r_long_range_B_refined 5.714 r_long_range_B_other 5.707 r_mcangle_it 4.109 r_mcangle_other 4.109 r_scangle_other 3.885 r_mcbond_it 3.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.649 r_dihedral_angle_4_deg 17.484 r_dihedral_angle_3_deg 16.813 r_dihedral_angle_1_deg 6.295 r_long_range_B_refined 5.714 r_long_range_B_other 5.707 r_mcangle_it 4.109 r_mcangle_other 4.109 r_scangle_other 3.885 r_mcbond_it 3.007 r_mcbond_other 3.006 r_scbond_it 2.748 r_scbond_other 2.747 r_angle_refined_deg 1.656 r_angle_other_deg 1.105 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3788 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 178
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling