3P9I

Crystal structure of perennial ryegrass LpOMT1 complexed with S-adenosyl-L-homocysteine and sinapaldehyde


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P9CPDB ENTRY 3P9C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52770.1 M sodium succinate, 28% (w/v) PEG monomethylether 5000, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, 5 mM sinapaldehyde, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.938α = 90
b = 85.225β = 111.1
c = 98.568γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2008-11-08SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0ALS8.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
11.8547.07195.70.0857.33.1139446
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.851.9591.40.3670.3671.72.416596

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3P9C1.8547.07139446697294.40.23180.2609random28.3449
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]
-14.076-0.24514.921-0.845
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it5.515
c_scbond_it4.212
c_mcangle_it3.764
c_mcbond_it2.883
c_angle_d1.194
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10760
Nucleic Acid Atoms
Solvent Atoms770
Heterogen Atoms196

Software

Software
Software NamePurpose
CNSrefinement
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection
MOSFLMdata reduction