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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC51 and manganese
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 10% PEG 4000, 20% glycerol
0.1M bicine Trizma pH 8.5
0.02M each of the carboxylic acids:
sodium formate
ammonium acetate
trisodiumm citrate
sodium potassium tartrate
sodium oxamate
Crystal Properties Matthews coefficient Solvent content 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.768 α = 103.66 b = 56.543 β = 103.34 c = 87 γ = 100.18
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 PILATUS 2M 2015-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.4 48.36 96.9 0.037 0.997 7.5 3.6 172755 9.2
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 1.4 1.48 95.3 0.778 1.3 3.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5JAZ (LC51) 1.4 30 164079 8662 96.93 0.18649 0.1854 0.20721 0.2086 RANDOM 16.583
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] -0.12 0.2 -0.38 0.67 -0.29 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.359 r_dihedral_angle_4_deg 14.975 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 5.362 r_long_range_B_refined 3.865 r_long_range_B_other 3.585 r_scangle_other 1.836 r_mcangle_it 1.443 r_mcangle_other 1.443 r_angle_refined_deg 1.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.359 r_dihedral_angle_4_deg 14.975 r_dihedral_angle_3_deg 12.337 r_dihedral_angle_1_deg 5.362 r_long_range_B_refined 3.865 r_long_range_B_other 3.585 r_scangle_other 1.836 r_mcangle_it 1.443 r_mcangle_other 1.443 r_angle_refined_deg 1.198 r_scbond_it 1.119 r_scbond_other 1.113 r_angle_other_deg 0.877 r_mcbond_it 0.827 r_mcbond_other 0.827 r_chiral_restr 0.073 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 573 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling O model building