6YJW

Structure of Fragaria ananassa O-methyltransferase crystallized with PAS polypeptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I71 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729312.5 % (w/v) PA200 0.1 M Hepes/NaOH 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
3.0159.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.932α = 90
b = 89.332β = 90
c = 150.897γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2017-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

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
12.134.7899.90.1010.1070.99918.298.8945670938.355
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)
12.12.299.91.0141.080.7062.468.624

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 REPLACEMENTTHROUGHOUT6I712.134.7853735297499.910.17320.17170.1996RANDOM34.811
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]
-0.091.2-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.509
r_dihedral_angle_3_deg15.297
r_dihedral_angle_4_deg15.088
r_dihedral_angle_1_deg6.252
r_angle_refined_deg1.56
r_angle_other_deg0.957
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.509
r_dihedral_angle_3_deg15.297
r_dihedral_angle_4_deg15.088
r_dihedral_angle_1_deg6.252
r_angle_refined_deg1.56
r_angle_other_deg0.957
r_chiral_restr0.079
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms417
Heterogen Atoms102

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing