4Q1A

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 6 {2-[5-(4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-1,3-thiazol-2-yl)-2-methoxyphenoxy]ethanol}


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
2.1743.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.665α = 90
b = 68.665β = 90
c = 120.36γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-01-31MSINGLE 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
11.93099.30.04420.644364343643
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92.0198.42.5462.96955

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 4JLN1.927.564138741387222499.230.20510.20510.202610.2501RANDOM40.208
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]
0.140.14-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.348
r_dihedral_angle_4_deg18.741
r_dihedral_angle_3_deg17.857
r_dihedral_angle_1_deg6.728
r_long_range_B_refined2.395
r_long_range_B_other2.378
r_scangle_other1.889
r_mcangle_it1.718
r_mcangle_other1.717
r_angle_refined_deg1.649
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.348
r_dihedral_angle_4_deg18.741
r_dihedral_angle_3_deg17.857
r_dihedral_angle_1_deg6.728
r_long_range_B_refined2.395
r_long_range_B_other2.378
r_scangle_other1.889
r_mcangle_it1.718
r_mcangle_other1.717
r_angle_refined_deg1.649
r_scbond_it1.533
r_scbond_other1.533
r_mcbond_it1.522
r_mcbond_other1.521
r_angle_other_deg0.957
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3784
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms110

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling