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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC56 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 293 10% PEG 4000, 20% glycerol
0.1M MOPS/HEPES-Na pH 7.5
0.03M of each NPS
(0.3M sodium nitrate, 0.3M disodium hydrogen phosphate, 0.3M ammonium sulfate)
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.755 α = 103.44 b = 55.951 β = 103.03 c = 85.619 γ = 100.49
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 2015-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.94572 ESRF ID23-1
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 1.8 48.11 95.3 0.081 0.081 0.996 7.4 3.1 77884 24.2
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 1.8 1.9 94.9 0.71 1.7 3.1
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) 1.8 30 73880 3933 95.18 0.17749 0.17592 0.183 0.2064 0.2121 RANDOM 29.013
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] -0.18 0.08 -0.71 0.8 -0.73 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.153 r_dihedral_angle_4_deg 15.762 r_dihedral_angle_3_deg 13.478 r_dihedral_angle_1_deg 5.405 r_long_range_B_refined 5.327 r_long_range_B_other 5.281 r_scangle_other 3.37 r_mcangle_it 2.549 r_mcangle_other 2.549 r_scbond_it 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.153 r_dihedral_angle_4_deg 15.762 r_dihedral_angle_3_deg 13.478 r_dihedral_angle_1_deg 5.405 r_long_range_B_refined 5.327 r_long_range_B_other 5.281 r_scangle_other 3.37 r_mcangle_it 2.549 r_mcangle_other 2.549 r_scbond_it 2.022 r_scbond_other 2.021 r_mcbond_it 1.543 r_mcbond_other 1.543 r_angle_refined_deg 1.239 r_angle_other_deg 0.882 r_chiral_restr 0.075 r_bond_refined_d 0.008 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 335 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling O model building