2FOI

Synthesis, Biological Activity, and X-Ray Crystal Structural Analysis of Diaryl Ether Inhibitors of Malarial Enoyl ACP Reductase.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NHD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62982.35 M (NH4)2SO4, 100 sodium acetate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.448.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.861α = 90
b = 130.861β = 90
c = 82.687γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IV2004-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

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
12.533.82528223997

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1NHD2.533.7723997128599.280.196550.196550.193430.25493RANDOM37.069
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.249
r_dihedral_angle_4_deg19.701
r_dihedral_angle_3_deg18.427
r_scangle_it7.718
r_scbond_it5.888
r_dihedral_angle_1_deg5.67
r_mcangle_it4.249
r_mcbond_it2.819
r_angle_refined_deg1.517
r_nbtor_refined0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.249
r_dihedral_angle_4_deg19.701
r_dihedral_angle_3_deg18.427
r_scangle_it7.718
r_scbond_it5.888
r_dihedral_angle_1_deg5.67
r_mcangle_it4.249
r_mcbond_it2.819
r_angle_refined_deg1.517
r_nbtor_refined0.336
r_symmetry_vdw_refined0.271
r_nbd_refined0.26
r_symmetry_hbond_refined0.243
r_xyhbond_nbd_refined0.202
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_refined
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 Atoms4576
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
AMoREphasing