1YHK

Trypanosoma cruzi farnesyl diphosphate synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherSelenomethionine replaced protein model (MAD)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION4.6293pH 4.6, LIQUID DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.347.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.925α = 90
b = 57.925β = 90
c = 397.697γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97929NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.165.9421828

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSelenomethionine replaced protein model (MAD)2.165.942182821828117293.950.175810.173080.22686RANDOM27.413
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]
0.560.280.56-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.954
r_dihedral_angle_1_deg5.644
r_scbond_it3.811
r_mcangle_it2.385
r_angle_refined_deg2.088
r_mcbond_it1.361
r_angle_other_deg1.056
r_symmetry_vdw_other0.327
r_nbd_other0.251
r_symmetry_vdw_refined0.234
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it5.954
r_dihedral_angle_1_deg5.644
r_scbond_it3.811
r_mcangle_it2.385
r_angle_refined_deg2.088
r_mcbond_it1.361
r_angle_other_deg1.056
r_symmetry_vdw_other0.327
r_nbd_other0.251
r_symmetry_vdw_refined0.234
r_nbd_refined0.231
r_symmetry_hbond_refined0.225
r_xyhbond_nbd_refined0.193
r_chiral_restr0.144
r_nbtor_other0.093
r_bond_refined_d0.031
r_gen_planes_refined0.012
r_gen_planes_other0.007
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2873
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing