6I73

Structure of Fragaria ananassa O-methyltransferase in complex with S-adenosylhomocysteine and protocatechuic aldehyde


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KYW 

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
2.6954.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.376α = 90
b = 87.655β = 90
c = 146.814γ = 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
11.3529.311000.090.0960.99915.378.8218779218.926
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)
11.351.4599.90.8820.950.6912.157.373

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 REPLACEMENTTHROUGHOUT1KYW1.3529.31184027376499.960.12220.12170.148RANDOM15.123
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]
0.18-0.560.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.276
r_dihedral_angle_4_deg22.998
r_sphericity_free19.522
r_dihedral_angle_3_deg11.698
r_sphericity_bonded7.391
r_dihedral_angle_1_deg6.277
r_rigid_bond_restr2.244
r_angle_refined_deg1.678
r_angle_other_deg1.136
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.276
r_dihedral_angle_4_deg22.998
r_sphericity_free19.522
r_dihedral_angle_3_deg11.698
r_sphericity_bonded7.391
r_dihedral_angle_1_deg6.277
r_rigid_bond_restr2.244
r_angle_refined_deg1.678
r_angle_other_deg1.136
r_chiral_restr0.096
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5398
Nucleic Acid Atoms
Solvent Atoms1014
Heterogen Atoms103

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing