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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC55 and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JAZ LC51, pdb code: 5JAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10% W/V PEG 8000, 20% V/V ethylene glycol,
0.1M MES/imidazole pH6.5
0.02M each monosaccharide,
(D-glucose, D-mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine)
Crystal Properties Matthews coefficient Solvent content 2.37 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.575 α = 103.84 b = 56.459 β = 103.25 c = 85.708 γ = 100.15
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 1.65 48.68 97.4 0.09 0.09 0.997 9 3.5 103882
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 1.65 1.74 95.9 0.633 1.8 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT LC51, pdb code: 5JAZ 1.65 30 98676 5192 97.44 0.18068 0.17944 0.1887 0.20379 0.2103 RANDOM 21.843
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] -0.78 -0.22 0.02 0.58 -1.17 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.517 r_dihedral_angle_4_deg 15.45 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 5.489 r_long_range_B_refined 4.495 r_long_range_B_other 4.353 r_scangle_other 2.349 r_mcangle_it 1.949 r_mcangle_other 1.949 r_scbond_it 1.394
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.517 r_dihedral_angle_4_deg 15.45 r_dihedral_angle_3_deg 13.052 r_dihedral_angle_1_deg 5.489 r_long_range_B_refined 4.495 r_long_range_B_other 4.353 r_scangle_other 2.349 r_mcangle_it 1.949 r_mcangle_other 1.949 r_scbond_it 1.394 r_scbond_other 1.394 r_angle_refined_deg 1.234 r_mcbond_it 1.131 r_mcbond_other 1.13 r_angle_other_deg 0.898 r_chiral_restr 0.076 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 482 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling O model building