4DWG

Crystal structure of Trypanosome cruzi farnesyl diphosphate synthase in complex with [2-(n-heptylamino)ethane-1,1-diyl]bisphosphonic acid and Mg2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YHLPDB ENTRY 1YHL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529112.5 mg/mL protein in 250 uM inhibitor, 250 uM IPP, 1 mM magnesium chloride, mother liquor: 100 mM sodium acetate, pH 4.6-5.2, 200 mM ammonium sulfate, 2-10% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3247.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.173α = 90
b = 58.173β = 90
c = 391.822γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-09-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.979NSLSX6A

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
12.0165.30497.80.0814.25.627252
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)
12.012.0498.70.3464.81281

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1YHL2.0139.88927229137098.160.20530.2020.266RANDOM29.1704
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]
0.590.30.59-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.024
r_dihedral_angle_4_deg17.004
r_dihedral_angle_3_deg15.742
r_dihedral_angle_1_deg5.498
r_scangle_it4.505
r_scbond_it3.086
r_angle_refined_deg1.861
r_mcangle_it1.705
r_mcbond_it0.988
r_chiral_restr0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.024
r_dihedral_angle_4_deg17.004
r_dihedral_angle_3_deg15.742
r_dihedral_angle_1_deg5.498
r_scangle_it4.505
r_scbond_it3.086
r_angle_refined_deg1.861
r_mcangle_it1.705
r_mcbond_it0.988
r_chiral_restr0.13
r_bond_refined_d0.02
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2882
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms49

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
REFMACphasing