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Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 9 {2-{[(1R)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-propyl-1,3-thiazol-4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine}
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 2.18 43.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.734 α = 90 b = 68.734 β = 90 c = 120.623 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 93 IMAGE PLATE RIGAKU RAXIS IV++ 2013-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 99.5 0.033 19.38 37712 37712
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 2.12 98.5 0.671 1.79 6015
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 27.39 35172 35172 1934 97.91 0.19437 0.19437 0.19099 0.1944 0.25365 0.2408 RANDOM 51.338
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] -4.5 -4.5 9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.917 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_4_deg 17.539 r_dihedral_angle_1_deg 7.248 r_long_range_B_refined 5.929 r_long_range_B_other 5.928 r_mcangle_it 4.704 r_mcangle_other 4.703 r_scangle_other 4.146 r_mcbond_it 3.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.917 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_4_deg 17.539 r_dihedral_angle_1_deg 7.248 r_long_range_B_refined 5.929 r_long_range_B_other 5.928 r_mcangle_it 4.704 r_mcangle_other 4.703 r_scangle_other 4.146 r_mcbond_it 3.458 r_mcbond_other 3.458 r_scbond_it 3.114 r_scbond_other 3.114 r_angle_other_deg 2.016 r_angle_refined_deg 1.676 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3726 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 112
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling