3P9K

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3P9IPDB ENTRY 3P9I

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52770.1 M sodium succinate, 28% (w/v) PEG 5000 monomethylether, 2 mM dithiothreitol, 2.5 mM S-adenosyl-L-homocysteine, 5 mM coniferaldehyde, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3748.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.375α = 90
b = 85.062β = 111.75
c = 98.586γ = 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
12.2548.69399.60.1187.13.678617
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)
2.252.3798.10.4390.4391.32.99920

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 3P9I2.2548.69378617395298.60.23160.262random34.915
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]
10.832-1.096-23.01912.187
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it4.561
c_scbond_it3.123
c_mcangle_it3.052
c_mcbond_it1.964
c_angle_d1.214
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10760
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms156

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
BOSdata collection
CNSphasing