5HXO

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase with D71M, E75A and H103Y Mutants


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72915% (w/v) PEG 8000, 40% MPD, 0.1 M Cacodylate, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.1643.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.683α = 90
b = 51.683β = 90
c = 173.561γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102014-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL12B21.0SPring-8BL12B2

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
12.052599.90.04342.810.615682
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)
12.052.1299.90.4129.6

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 REPLACEMENTTHROUGHOUT1JP32.0524.781481277799.770.193380.191130.23646RANDOM27.691
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]
-0.22-0.220.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.221
r_dihedral_angle_4_deg15.356
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg5.868
r_long_range_B_refined5.02
r_long_range_B_other4.876
r_scangle_other2.999
r_mcangle_it2.271
r_mcangle_other2.27
r_scbond_it1.823
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.221
r_dihedral_angle_4_deg15.356
r_dihedral_angle_3_deg14.337
r_dihedral_angle_1_deg5.868
r_long_range_B_refined5.02
r_long_range_B_other4.876
r_scangle_other2.999
r_mcangle_it2.271
r_mcangle_other2.27
r_scbond_it1.823
r_scbond_other1.822
r_mcbond_it1.387
r_mcbond_other1.387
r_angle_refined_deg1.214
r_angle_other_deg0.743
r_chiral_restr0.066
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 Atoms1755
Nucleic Acid Atoms
Solvent Atoms118
Heterogen Atoms

Software

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