4Q18

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]


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
2.2144.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.75α = 90
b = 68.75β = 90
c = 122.45γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-11-20MSINGLE 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
123099.40.05913.63811938119
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)
122.199.90.5472.755189

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 4JLN227.973619436194192499.380.184850.184850.183080.21613RANDOM46.465
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]
-2.98-2.985.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.649
r_dihedral_angle_4_deg17.484
r_dihedral_angle_3_deg16.813
r_dihedral_angle_1_deg6.295
r_long_range_B_refined5.714
r_long_range_B_other5.707
r_mcangle_it4.109
r_mcangle_other4.109
r_scangle_other3.885
r_mcbond_it3.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.649
r_dihedral_angle_4_deg17.484
r_dihedral_angle_3_deg16.813
r_dihedral_angle_1_deg6.295
r_long_range_B_refined5.714
r_long_range_B_other5.707
r_mcangle_it4.109
r_mcangle_other4.109
r_scangle_other3.885
r_mcbond_it3.007
r_mcbond_other3.006
r_scbond_it2.748
r_scbond_other2.747
r_angle_refined_deg1.656
r_angle_other_deg1.105
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3788
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms178

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling