5JAZ

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC51 and manganese


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529310% PEG 4000, 20% glycerol 0.1M bicine Trizma pH 8.5 0.02M each of the carboxylic acids: sodium formate ammonium acetate trisodiumm citrate sodium potassium tartrate sodium oxamate
Crystal Properties
Matthews coefficientSolvent content
2.4349.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.768α = 103.66
b = 56.543β = 103.34
c = 87γ = 100.18
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)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
11.448.3696.90.0370.9977.53.61727559.2
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)
11.41.4895.30.7781.33.5

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 SYNTHESISTHROUGHOUT5JAZ (LC51)1.430164079866296.930.186490.18540.20721RANDOM16.583
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]
-0.120.2-0.380.67-0.29-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.359
r_dihedral_angle_4_deg14.975
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg5.362
r_long_range_B_refined3.865
r_long_range_B_other3.585
r_scangle_other1.836
r_mcangle_it1.443
r_mcangle_other1.443
r_angle_refined_deg1.198
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.359
r_dihedral_angle_4_deg14.975
r_dihedral_angle_3_deg12.337
r_dihedral_angle_1_deg5.362
r_long_range_B_refined3.865
r_long_range_B_other3.585
r_scangle_other1.836
r_mcangle_it1.443
r_mcangle_other1.443
r_angle_refined_deg1.198
r_scbond_it1.119
r_scbond_other1.113
r_angle_other_deg0.877
r_mcbond_it0.827
r_mcbond_other0.827
r_chiral_restr0.073
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 Atoms573
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Omodel building