7ZI6

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0325 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52851.1 M Sodium citrate, 73 mM HEPES
Crystal Properties
Matthews coefficientSolvent content
2.2144.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.629α = 90
b = 68.629β = 90
c = 122.72γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.975631SOLEILPROXIMA 2

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
12.148.53980.1070.110.99919.6525.7971750857.632
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)
12.12.2396.81.9181.9550.751.926.742

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 REPLACEMENTTHROUGHOUT4KCG2.148.531659787498.030.19790.19580.236RANDOM55.748
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]
0.860.86-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.858
r_dihedral_angle_3_deg16.66
r_dihedral_angle_4_deg15.007
r_dihedral_angle_1_deg6.644
r_angle_refined_deg1.593
r_angle_other_deg1.309
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.858
r_dihedral_angle_3_deg16.66
r_dihedral_angle_4_deg15.007
r_dihedral_angle_1_deg6.644
r_angle_refined_deg1.593
r_angle_other_deg1.309
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1915
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing