7ZI8

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0602 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
Crystal Properties
Matthews coefficientSolvent content
2.1843.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.618α = 90
b = 68.618β = 90
c = 121.247γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980112SOLEILPROXIMA 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
11.9948.5299.90.1180.120.99918.9925.4932044658.247
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)
11.992.1199.33.3873.4590.410.8724.524

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 REPLACEMENTTHROUGHOUT4KCG1.9948.5219423102399.880.20440.20140.2634RANDOM54.954
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]
-0.33-0.330.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.123
r_dihedral_angle_4_deg17.729
r_dihedral_angle_3_deg16.084
r_dihedral_angle_1_deg6.458
r_angle_refined_deg1.533
r_angle_other_deg1.328
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.123
r_dihedral_angle_4_deg17.729
r_dihedral_angle_3_deg16.084
r_dihedral_angle_1_deg6.458
r_angle_refined_deg1.533
r_angle_other_deg1.328
r_chiral_restr0.076
r_bond_refined_d0.008
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 Atoms1915
Nucleic Acid Atoms
Solvent Atoms32
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing