7WH9

holo structure of emodin 1-OH O-methyltransferase complex with emodin and S-Adenosyl-L-homocysteine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7289.151.8M triamine citrate
2VAPOR DIFFUSION, SITTING DROP6289.151.8M triamine citrate
Crystal Properties
Matthews coefficientSolvent content
2.8858.13
2.1743.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 162.093α = 90
b = 162.093β = 90
c = 130.219γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-04-18MSINGLE WAVELENGTH
21x-ray100PIXELDECTRIS EIGER X 16M2019-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.979SSRFBL19U1
2SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.83099.90.1090.1150.0350.99724.510.348697
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.91000.5010.5260.1610.944.510.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.80327.29171.3448503199499.570.17660.17480.217261.6619
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.451
f_angle_d1.327
f_chiral_restr0.083
f_bond_d0.011
f_plane_restr0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10992
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms138

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
xia2data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
xia2data reduction
PHASERphasing
AutoSolphasing