4Q1C

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 8 {2,2'-[{4-[(2R)-4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-2,3-dihydro-1,3-thiazol-2-yl]benzene-1,2-diyl}bis(oxy)]diethanol}


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
2.1542.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.661α = 90
b = 68.661β = 90
c = 119.277γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2013-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9785APS21-ID-G

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
123098.80.05116.573690236902
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)
122.1296.10.7162.045748

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 4JLN225.983475034750186498.110.207140.207140.205370.23832RANDOM29.189
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]
-2.19-2.194.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.512
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg17.818
r_dihedral_angle_1_deg7.178
r_angle_other_deg2.403
r_angle_refined_deg1.723
r_long_range_B_refined0.429
r_long_range_B_other0.427
r_mcangle_it0.385
r_mcangle_other0.385
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.512
r_dihedral_angle_4_deg18.318
r_dihedral_angle_3_deg17.818
r_dihedral_angle_1_deg7.178
r_angle_other_deg2.403
r_angle_refined_deg1.723
r_long_range_B_refined0.429
r_long_range_B_other0.427
r_mcangle_it0.385
r_mcangle_other0.385
r_mcbond_it0.368
r_mcbond_other0.368
r_scangle_other0.361
r_scbond_it0.34
r_scbond_other0.34
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3757
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms114

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling