8X35

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


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
2.1141.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.31α = 90
b = 49.23β = 91.067
c = 121.39γ = 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)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
11.92501000.9949.711.744740
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)
11.922.041003.10.7711.0712

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-VALUE7VPC1.9249.14644740223799.9890.2210.2190.256649.366
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]
-2.0840.0565.321-3.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.347
r_dihedral_angle_6_deg17.857
r_lrange_it6.731
r_lrange_other6.729
r_scangle_it5.744
r_scangle_other5.743
r_dihedral_angle_1_deg5.725
r_dihedral_angle_2_deg5.549
r_scbond_it4.086
r_scbond_other4.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg18.347
r_dihedral_angle_6_deg17.857
r_lrange_it6.731
r_lrange_other6.729
r_scangle_it5.744
r_scangle_other5.743
r_dihedral_angle_1_deg5.725
r_dihedral_angle_2_deg5.549
r_scbond_it4.086
r_scbond_other4.085
r_mcangle_other3.892
r_mcangle_it3.89
r_mcbond_it2.846
r_mcbond_other2.846
r_angle_refined_deg1.566
r_angle_other_deg0.735
r_nbd_other0.267
r_symmetry_nbd_refined0.232
r_nbd_refined0.22
r_symmetry_nbd_other0.22
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.156
r_symmetry_xyhbond_nbd_other0.134
r_symmetry_nbtor_other0.079
r_chiral_restr0.069
r_metal_ion_refined0.043
r_symmetry_xyhbond_nbd_refined0.035
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_other_2_deg0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3778
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
XDSdata scaling
PHASERphasing