6I72

Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine and caffeic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I73 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.4-0.6 M Ammonium sulfate, 1 M Lithium sulfate, 0.1 M Sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.754.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.258α = 90
b = 87.728β = 90
c = 147.475γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2017-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8943BESSY14.3

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
11.529.36990.070.0740.99919.559.2613650026.484
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)
11.51.698.10.9691.0250.7932.389.463

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 REPLACEMENTTHROUGHOUT6I731.529.36133748275198.970.15240.15190.173RANDOM23.02
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]
-1.330.460.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.455
r_dihedral_angle_4_deg16.577
r_dihedral_angle_3_deg12.883
r_dihedral_angle_1_deg6.26
r_angle_refined_deg1.692
r_angle_other_deg1.122
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.455
r_dihedral_angle_4_deg16.577
r_dihedral_angle_3_deg12.883
r_dihedral_angle_1_deg6.26
r_angle_refined_deg1.692
r_angle_other_deg1.122
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5388
Nucleic Acid Atoms
Solvent Atoms727
Heterogen Atoms109

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing