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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC54 and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JAZ 5JAZ (LC51)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 LC54 - E11
10% PEG 4000, 20% glycerol
0.1M bicine Trizma pH 8.5
0.03M of each ethylene glycol
(0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol)
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.473 α = 103.1 b = 56.035 β = 102.89 c = 86.041 γ = 100.9
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2015-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97239 ESRF ID29
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 48.55 94.3 0.076 0.076 0.998 10.1 3.7 109929 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 92.7 0.8 1.6 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5JAZ (LC51) 1.6 30 104390 5526 94.31 0.17917 0.17811 0.1871 0.19908 0.2037 RANDOM 23.242
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] -0.17 0.31 -0.51 0.72 -0.5 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 16.994 r_dihedral_angle_3_deg 13.274 r_dihedral_angle_1_deg 5.404 r_long_range_B_refined 5.138 r_long_range_B_other 4.95 r_scangle_other 2.414 r_mcangle_it 2.181 r_mcangle_other 2.181 r_scbond_it 1.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.971 r_dihedral_angle_4_deg 16.994 r_dihedral_angle_3_deg 13.274 r_dihedral_angle_1_deg 5.404 r_long_range_B_refined 5.138 r_long_range_B_other 4.95 r_scangle_other 2.414 r_mcangle_it 2.181 r_mcangle_other 2.181 r_scbond_it 1.452 r_scbond_other 1.452 r_mcbond_it 1.24 r_mcbond_other 1.24 r_angle_refined_deg 1.191 r_angle_other_deg 0.872 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6552 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement XDS data processing SCALA data scaling O model building