5JBI

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC52 and manganese


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JAZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310% PEG 8000, 20%ethylene glycol 0.1M MES/imidazole, pH 6.5 0.02M each alcohol: 1,6-hexanediol 1-butanol (RS)-1,2-propanediol 2-propanol 1,4-butanediol 1,3-propanediol
Crystal Properties
Matthews coefficientSolvent content
2.4249.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.657α = 103.6
b = 56.397β = 102.96
c = 85.919γ = 100.46
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
11.748.7897.80.0920.0920.9967.93.69583318.5
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)
11.71.7996.50.7621.83.5

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 SYNTHESISTHROUGHOUT5JAZ1.73091006480097.810.180890.179330.21014RANDOM25.645
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]
-1.040.070.050.42-1.030.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.083
r_dihedral_angle_4_deg14.288
r_dihedral_angle_3_deg13.544
r_dihedral_angle_1_deg5.418
r_long_range_B_refined4.657
r_long_range_B_other4.518
r_scangle_other2.778
r_mcangle_it2.109
r_mcangle_other2.109
r_scbond_it1.667
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.083
r_dihedral_angle_4_deg14.288
r_dihedral_angle_3_deg13.544
r_dihedral_angle_1_deg5.418
r_long_range_B_refined4.657
r_long_range_B_other4.518
r_scangle_other2.778
r_mcangle_it2.109
r_mcangle_other2.109
r_scbond_it1.667
r_scbond_other1.666
r_mcbond_it1.271
r_mcbond_other1.271
r_angle_refined_deg1.213
r_angle_other_deg0.888
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms458
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Omodel building