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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC52 and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10% PEG 8000, 20%ethylene glycol
0.1M MES/imidazole, pH 6.5
0.02M each alcohol:
1,6-hexanediol
1-butanol
(RS)-1,2-propanediol
2-propanol
1,4-butanediol
1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.42 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.657 α = 103.6 b = 56.397 β = 102.96 c = 85.919 γ = 100.46
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) 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 1.7 48.78 97.8 0.092 0.092 0.996 7.9 3.6 95833 18.5
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 1.7 1.79 96.5 0.762 1.8 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5JAZ 1.7 30 91006 4800 97.81 0.18089 0.17933 0.1869 0.21014 0.2189 RANDOM 25.645
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] -1.04 0.07 0.05 0.42 -1.03 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_dihedral_angle_4_deg 14.288 r_dihedral_angle_3_deg 13.544 r_dihedral_angle_1_deg 5.418 r_long_range_B_refined 4.657 r_long_range_B_other 4.518 r_scangle_other 2.778 r_mcangle_it 2.109 r_mcangle_other 2.109 r_scbond_it 1.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_dihedral_angle_4_deg 14.288 r_dihedral_angle_3_deg 13.544 r_dihedral_angle_1_deg 5.418 r_long_range_B_refined 4.657 r_long_range_B_other 4.518 r_scangle_other 2.778 r_mcangle_it 2.109 r_mcangle_other 2.109 r_scbond_it 1.667 r_scbond_other 1.666 r_mcbond_it 1.271 r_mcbond_other 1.271 r_angle_refined_deg 1.213 r_angle_other_deg 0.888 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 458 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling O model building