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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC176, and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AU8
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, 0.02M each of sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine, 0.1M mes/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.38 48.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.57 α = 104.11 b = 56.465 β = 103.25 c = 86.024 γ = 100.16
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 PSI PILATUS 6M mirrors 2014-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97856 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 79.97 94.2 0.08 8.2 3.4 110454 110454
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 90.3 0.478 2.1 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 3AU8 1.6 48.65 104856 5530 94.18 0.17807 0.1766 0.1863 0.2062 0.2152 RANDOM 22.628
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] -1.03 -0.71 0.23 0.07 -1.59 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.499 r_dihedral_angle_3_deg 16.587 r_dihedral_angle_4_deg 14.58 r_long_range_B_refined 5.773 r_long_range_B_other 5.586 r_dihedral_angle_1_deg 5.525 r_scangle_other 3.47 r_mcangle_it 2.321 r_mcangle_other 2.321 r_scbond_it 2.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.499 r_dihedral_angle_3_deg 16.587 r_dihedral_angle_4_deg 14.58 r_long_range_B_refined 5.773 r_long_range_B_other 5.586 r_dihedral_angle_1_deg 5.525 r_scangle_other 3.47 r_mcangle_it 2.321 r_mcangle_other 2.321 r_scbond_it 2.128 r_scbond_other 2.127 r_mcbond_it 1.482 r_mcbond_other 1.481 r_angle_refined_deg 1.329 r_angle_other_deg 0.766 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 714 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing