4Q1D

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}


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JLNPDB entry 4JLN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52851.5 M trisodium citrate dehydrate and 25 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.1843.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.734α = 90
b = 68.734β = 90
c = 120.623γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IV++2013-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
123099.50.03319.383771237712
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1298.50.6711.796015

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4JLN227.393517235172193497.910.194370.194370.190990.25365RANDOM51.338
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]
-4.5-4.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.917
r_dihedral_angle_3_deg18.446
r_dihedral_angle_4_deg17.539
r_dihedral_angle_1_deg7.248
r_long_range_B_refined5.929
r_long_range_B_other5.928
r_mcangle_it4.704
r_mcangle_other4.703
r_scangle_other4.146
r_mcbond_it3.458
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.917
r_dihedral_angle_3_deg18.446
r_dihedral_angle_4_deg17.539
r_dihedral_angle_1_deg7.248
r_long_range_B_refined5.929
r_long_range_B_other5.928
r_mcangle_it4.704
r_mcangle_other4.703
r_scangle_other4.146
r_mcbond_it3.458
r_mcbond_other3.458
r_scbond_it3.114
r_scbond_other3.114
r_angle_other_deg2.016
r_angle_refined_deg1.676
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3726
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms112

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling