1YHL

Structure of the complex of Trypanosoma cruzi farnesyl diphosphate synthase with risedronate, dmapp and mg+2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION4.6295pH 4.6, LIQUID DIFFUSION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3147

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.152α = 90
b = 58.152β = 90
c = 389.512γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.964.5598.10.0870.08712.48.929502

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT1.9564.5527981149798.090.176570.173570.23223RANDOM25.746
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]
0.390.190.39-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.558
r_dihedral_angle_4_deg22.245
r_dihedral_angle_3_deg15.473
r_dihedral_angle_1_deg6.525
r_scangle_it5.113
r_scbond_it3.547
r_angle_refined_deg2.248
r_mcangle_it2.069
r_mcbond_it1.58
r_symmetry_hbond_refined0.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.558
r_dihedral_angle_4_deg22.245
r_dihedral_angle_3_deg15.473
r_dihedral_angle_1_deg6.525
r_scangle_it5.113
r_scbond_it3.547
r_angle_refined_deg2.248
r_mcangle_it2.069
r_mcbond_it1.58
r_symmetry_hbond_refined0.378
r_nbtor_refined0.312
r_symmetry_vdw_refined0.286
r_chiral_restr0.28
r_nbd_refined0.256
r_xyhbond_nbd_refined0.232
r_metal_ion_refined0.035
r_bond_refined_d0.027
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_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 Atoms2891
Nucleic Acid Atoms
Solvent Atoms392
Heterogen Atoms39

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CCP4data scaling
AMoREphasing