7ZI7

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0345 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52850.95 M Sodium citrate, 63 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
2.1743.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.627α = 90
b = 68.627β = 90
c = 120.601γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2020-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.980111SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.848.531000.0670.0680.99926.1262733847.024
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.911001.3721.39280.8342.2427.159

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 REPLACEMENTTHROUGHOUT4KCG1.848.5325971136799.980.18940.18730.2271RANDOM43.757
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]
-0.59-0.591.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.06
r_dihedral_angle_4_deg16.089
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.658
r_angle_other_deg1.395
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.06
r_dihedral_angle_4_deg16.089
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg6.173
r_angle_refined_deg1.658
r_angle_other_deg1.395
r_chiral_restr0.078
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1923
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing