5HXQ

Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants) Complexed with DMSPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HXN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529113% PEG 10K, 20mM 18-crown-6, 0.1M MES, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.448.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.752α = 90
b = 66.8β = 90
c = 128.726γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 3152015-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11.0NSRRCBL15A1

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
11.952599.30.04342.45.938064
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)
11.952.0299.80.765.7

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 REPLACEMENTTHROUGHOUT5HXN1.952531779167987.280.19640.193970.24128RANDOM30.882
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]
-0.461.26-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.174
r_dihedral_angle_3_deg14.87
r_dihedral_angle_4_deg13.638
r_long_range_B_refined5.844
r_long_range_B_other5.561
r_dihedral_angle_1_deg5.529
r_scangle_other3.085
r_mcangle_other2.467
r_mcangle_it2.466
r_scbond_it1.844
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.174
r_dihedral_angle_3_deg14.87
r_dihedral_angle_4_deg13.638
r_long_range_B_refined5.844
r_long_range_B_other5.561
r_dihedral_angle_1_deg5.529
r_scangle_other3.085
r_mcangle_other2.467
r_mcangle_it2.466
r_scbond_it1.844
r_scbond_other1.844
r_mcbond_it1.479
r_mcbond_other1.477
r_angle_refined_deg1.246
r_angle_other_deg1.129
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.003
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 Atoms3639
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms50

Software

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