6YUH

Crystal structure of SMYD3 with diperodon R enantiomer bound to allosteric site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MEK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.25293Tris buffer 0.1 M, pH 8.25 Magnesium acetate 0.1 M PEG3350 16%
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.142α = 90
b = 66.284β = 90
c = 105.949γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-10-02MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX IV BEAMLINE BioMAX1.8MAX IVBioMAX

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
11.93105.951000.1920.2030.9969.999.33260621.45
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.981001.7880.5151.69.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3MEK1.9352.31.3332606305499.820.18830.18610.229528.0359
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]
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3402
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms77

Software

Software
Software NamePurpose
PHENIXrefinement
REFMACrefinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction