5JMW

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JAZ5JAZ (LC51)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529312.5% W/V PEG 1000, 12.5% PEG 3350, 12.5% v/v MPD 0.03M of each ethylene glycol 0.1M MOPS/HEPES-Na pH 7.5 (0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol)
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.43α = 103.57
b = 56.193β = 103.07
c = 86.046γ = 100.4
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979490DiamondI02

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
11.5528.9696.40.0710.99810.23.612367613
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)
11.551.5887.90.491.73.3

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)1.5528117573609996.350.181430.180360.20204RANDOM18.657
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]
-0.190.2-0.81.02-0.42-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.113
r_dihedral_angle_4_deg21.001
r_dihedral_angle_3_deg12.547
r_dihedral_angle_1_deg5.547
r_long_range_B_refined3.828
r_long_range_B_other3.626
r_scangle_other1.71
r_mcangle_it1.494
r_mcangle_other1.494
r_angle_refined_deg1.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.113
r_dihedral_angle_4_deg21.001
r_dihedral_angle_3_deg12.547
r_dihedral_angle_1_deg5.547
r_long_range_B_refined3.828
r_long_range_B_other3.626
r_scangle_other1.71
r_mcangle_it1.494
r_mcangle_other1.494
r_angle_refined_deg1.176
r_scbond_it1.017
r_scbond_other1.017
r_angle_other_deg0.867
r_mcbond_it0.849
r_mcbond_other0.849
r_chiral_restr0.072
r_bond_refined_d0.007
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 Atoms545
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Omodel building