5HXN

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M and E75A mutants) from the Wild Tomato Solanum habrochaites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JP3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION829170% 2-Methyl-2,4-pentanediol (MPD), 0.1 M Tris, pH 8.0.
Crystal Properties
Matthews coefficientSolvent content
2.1843.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.891α = 90
b = 51.891β = 90
c = 173.286γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 315r2013-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.052597.40.04452.31115386
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1294.60.4954.310

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JP32.0523.221433775195.950.194130.191630.24135RANDOM28.296
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]
-0.06-0.060.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.724
r_dihedral_angle_3_deg15.894
r_dihedral_angle_4_deg13.301
r_dihedral_angle_1_deg5.659
r_long_range_B_refined5.261
r_long_range_B_other4.9
r_scangle_other2.835
r_mcangle_it2.25
r_mcangle_other2.249
r_scbond_it1.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.724
r_dihedral_angle_3_deg15.894
r_dihedral_angle_4_deg13.301
r_dihedral_angle_1_deg5.659
r_long_range_B_refined5.261
r_long_range_B_other4.9
r_scangle_other2.835
r_mcangle_it2.25
r_mcangle_other2.249
r_scbond_it1.696
r_scbond_other1.696
r_mcbond_other1.35
r_mcbond_it1.349
r_angle_refined_deg1.159
r_angle_other_deg0.735
r_chiral_restr0.063
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1771
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPphasing