7ZI1

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the dCKi1 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KCG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52850.9 M Sodium citrate, 60 mM HEPES, pH 7.5,
Crystal Properties
Matthews coefficientSolvent content
2.1843.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.625α = 90
b = 68.625β = 90
c = 120.809γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.97625ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
11.8548.531000.1880.0576.110.82542027.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.8898.92.050.60.611.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4KCG1.8548.5324091126799.860.20410.20250.2339RANDOM35.514
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]
-0.87-0.871.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.241
r_dihedral_angle_4_deg18.034
r_dihedral_angle_3_deg14.147
r_dihedral_angle_1_deg5.993
r_angle_refined_deg1.573
r_angle_other_deg1.348
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.241
r_dihedral_angle_4_deg18.034
r_dihedral_angle_3_deg14.147
r_dihedral_angle_1_deg5.993
r_angle_refined_deg1.573
r_angle_other_deg1.348
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1907
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing