4DWB

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DWGPDB ENTRY 4DWG

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
2.346.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.871α = 90
b = 57.871β = 90
c = 392.442γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-02-02MSINGLE 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
12.165.40793.20.1138.97.622705
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)
12.12.1498.20.5096.71158

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 4DWG2.119.89122545115692.820.2210.21780.2789RANDOM31.5472
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]
1.890.941.89-2.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.759
r_dihedral_angle_4_deg19.269
r_dihedral_angle_3_deg17.712
r_dihedral_angle_1_deg6.003
r_scangle_it4.319
r_scbond_it3
r_angle_refined_deg1.778
r_mcangle_it1.678
r_mcbond_it1
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.759
r_dihedral_angle_4_deg19.269
r_dihedral_angle_3_deg17.712
r_dihedral_angle_1_deg6.003
r_scangle_it4.319
r_scbond_it3
r_angle_refined_deg1.778
r_mcangle_it1.678
r_mcbond_it1
r_chiral_restr0.113
r_bond_refined_d0.021
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2882
Nucleic Acid Atoms
Solvent Atoms89
Heterogen Atoms48

Software

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