8X36

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP, IPP, and magnesium ion (form B)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VPC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293DL-malic acid, PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.3848.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.52α = 90
b = 48.68β = 90.69
c = 121.13γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 9M2021-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.0SPring-8BL32XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.285099.80.250.9898.7562617253.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.4299.74.670.5211.316.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7VPC2.2848.761.3326057130499.340.19680.1940.252164.42
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.6364
f_angle_d1.0228
f_chiral_restr0.0506
f_bond_d0.0075
f_plane_restr0.0074
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3796
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
XDSdata scaling
PHASERphasing