5JC1

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC55 and manganese


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310% W/V PEG 8000, 20% V/V ethylene glycol, 0.1M MES/imidazole pH6.5 0.02M each monosaccharide, (D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine)
Crystal Properties
Matthews coefficientSolvent content
2.3748.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.575α = 103.84
b = 56.459β = 103.25
c = 85.708γ = 100.15
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)CC (Half)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
11.6548.6897.40.090.090.99793.5103882
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)
11.651.7495.90.6331.83.4

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTLC51, pdb code: 5JAZ1.653098676519297.440.180680.179440.20379RANDOM21.843
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]
-0.78-0.220.020.58-1.170.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.517
r_dihedral_angle_4_deg15.45
r_dihedral_angle_3_deg13.052
r_dihedral_angle_1_deg5.489
r_long_range_B_refined4.495
r_long_range_B_other4.353
r_scangle_other2.349
r_mcangle_it1.949
r_mcangle_other1.949
r_scbond_it1.394
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.517
r_dihedral_angle_4_deg15.45
r_dihedral_angle_3_deg13.052
r_dihedral_angle_1_deg5.489
r_long_range_B_refined4.495
r_long_range_B_other4.353
r_scangle_other2.349
r_mcangle_it1.949
r_mcangle_other1.949
r_scbond_it1.394
r_scbond_other1.394
r_angle_refined_deg1.234
r_mcbond_it1.131
r_mcbond_other1.13
r_angle_other_deg0.898
r_chiral_restr0.076
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6552
Nucleic Acid Atoms
Solvent Atoms482
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Omodel building