4Q1B

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 7 {N-(2-(3-(4-(((4,6-diaminopyrimidin-2-yl)thio)methyl)-5-propylthiazol-2-yl)phenoxy)ethyl)methanesulfonamide}


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
2.2244.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.968α = 90
b = 68.968β = 90
c = 121.944γ = 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
12.153098.30.05217.423047230472
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)
12.152.2897.40.5522.874838

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 4JLN2.1527.522834928349154096.490.177050.177050.172980.25269RANDOM54.141
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]
-3.34-3.346.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.478
r_dihedral_angle_3_deg19.917
r_dihedral_angle_4_deg16.522
r_long_range_B_refined8.036
r_dihedral_angle_1_deg7.238
r_mcangle_it5.598
r_scbond_it4.139
r_mcbond_it4.026
r_angle_refined_deg1.696
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.478
r_dihedral_angle_3_deg19.917
r_dihedral_angle_4_deg16.522
r_long_range_B_refined8.036
r_dihedral_angle_1_deg7.238
r_mcangle_it5.598
r_scbond_it4.139
r_mcbond_it4.026
r_angle_refined_deg1.696
r_chiral_restr0.109
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3736
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms114

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling