5JMP

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC57 and manganese


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JAZLC51, 5JAZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310% W/V PEG 8000, 20% V/V ethylene glycol, 0.1 M MES/imidazole pH6.5 0.02M amino amino acid ( 0.2M sodium L-glutamate, 0.2M DL-alanine, 0.2M glycine, 0.2M DL-lysine HCL, 0.2M DL serine)
Crystal Properties
Matthews coefficientSolvent content
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.718α = 104.13
b = 56.58β = 103.33
c = 85.66γ = 100.12
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)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
11.741.3797.80.0950.0957.43.69560813.8
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)
11.71.7996.60.6023.7

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, 5JAZ1.73590831476197.790.179550.178060.20824RANDOM20.914
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]
-0.51-0.470.060.56-1.30.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.624
r_dihedral_angle_4_deg13.54
r_dihedral_angle_3_deg13.023
r_dihedral_angle_1_deg5.502
r_long_range_B_refined4.467
r_long_range_B_other4.303
r_scangle_other2.184
r_mcangle_it1.818
r_mcangle_other1.818
r_scbond_it1.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.624
r_dihedral_angle_4_deg13.54
r_dihedral_angle_3_deg13.023
r_dihedral_angle_1_deg5.502
r_long_range_B_refined4.467
r_long_range_B_other4.303
r_scangle_other2.184
r_mcangle_it1.818
r_mcangle_other1.818
r_scbond_it1.299
r_scbond_other1.298
r_angle_refined_deg1.203
r_mcbond_it1.057
r_mcbond_other1.054
r_angle_other_deg0.883
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 Atoms517
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
Omodel building