4Y6R

Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC137, and manganese


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310% w/v PEG 20,000, 20% v/v PEG MME 5502, 0.02M each of D-glucose, D- mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine, 0.1 M mes/imidazole pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.399α = 89.64
b = 54.852β = 105.4
c = 85.208γ = 107.61
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fmirrors2014-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97856ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.947.0895.50.1489.25.564132
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)
11.92950.79825.7

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 REPLACEMENTTHROUGHOUT4Y671.947.0860876325695.480.189040.187480.21789RANDOM29.577
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]
-1.822.07-0.53.070.52-2.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.525
r_dihedral_angle_4_deg23.428
r_dihedral_angle_3_deg16.721
r_dihedral_angle_1_deg5.4
r_long_range_B_refined4.722
r_long_range_B_other4.645
r_scangle_other2.987
r_mcangle_it2.203
r_mcangle_other2.203
r_scbond_it1.779
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.525
r_dihedral_angle_4_deg23.428
r_dihedral_angle_3_deg16.721
r_dihedral_angle_1_deg5.4
r_long_range_B_refined4.722
r_long_range_B_other4.645
r_scangle_other2.987
r_mcangle_it2.203
r_mcangle_other2.203
r_scbond_it1.779
r_scbond_other1.765
r_angle_refined_deg1.364
r_mcbond_it1.341
r_mcbond_other1.34
r_angle_other_deg1.23
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.004
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 Atoms454
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling