8X37

Neryl diphosphate synthase from Solanum lycopersicum complexed with DMSAPP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG3350, DL-Malic acid
Crystal Properties
Matthews coefficientSolvent content
2.4650.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.26α = 90
b = 50.27β = 91.327
c = 120.25γ = 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
11.98501000.1240.9938.526.641220
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)
11.982.081002.650.751.056.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7VPC1.9849.16541220206199.9440.2240.22130.274464.711
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]
-2.420.6247.077-4.681
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.413
r_dihedral_angle_6_deg15.29
r_lrange_other11.086
r_lrange_it11.084
r_scangle_it9.083
r_scangle_other9.082
r_mcangle_it6.969
r_mcangle_other6.969
r_dihedral_angle_2_deg6.061
r_dihedral_angle_1_deg6.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.413
r_dihedral_angle_6_deg15.29
r_lrange_other11.086
r_lrange_it11.084
r_scangle_it9.083
r_scangle_other9.082
r_mcangle_it6.969
r_mcangle_other6.969
r_dihedral_angle_2_deg6.061
r_dihedral_angle_1_deg6.016
r_scbond_it5.953
r_scbond_other5.952
r_mcbond_it4.948
r_mcbond_other4.947
r_angle_refined_deg1.471
r_angle_other_deg0.745
r_symmetry_nbd_refined0.43
r_nbd_other0.271
r_nbd_refined0.228
r_symmetry_nbd_other0.216
r_xyhbond_nbd_refined0.192
r_nbtor_refined0.179
r_symmetry_xyhbond_nbd_refined0.141
r_ncsr_local_group_10.137
r_symmetry_xyhbond_nbd_other0.097
r_symmetry_nbtor_other0.078
r_chiral_restr0.068
r_metal_ion_refined0.038
r_gen_planes_other0.007
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3818
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
XDSdata scaling
PHASERphasing