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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC134, and manganese
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 10% w/v PEG 20,000 20% v/v PEG MME 550, 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 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.396 α = 89.41 b = 54.963 β = 105.52 c = 85.054 γ = 107.28
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 6M-F mirrors 2014-11-24 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 2.1 47.15 93.9 0.085 10.7 4.1 46811
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 2.1 2.21 91.3 0.335 3.7 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.1 47.15 44433 2377 93.92 0.21859 0.21676 0.2165 0.25242 0.2523 RANDOM 33.495
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] -2.58 1.82 -1.3 5.11 -0.53 -3.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.225 r_dihedral_angle_3_deg 17.37 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_1_deg 5.803 r_long_range_B_refined 4.229 r_long_range_B_other 4.185 r_scangle_other 2.457 r_mcangle_it 2.251 r_mcangle_other 2.251 r_scbond_it 1.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.225 r_dihedral_angle_3_deg 17.37 r_dihedral_angle_4_deg 16.367 r_dihedral_angle_1_deg 5.803 r_long_range_B_refined 4.229 r_long_range_B_other 4.185 r_scangle_other 2.457 r_mcangle_it 2.251 r_mcangle_other 2.251 r_scbond_it 1.374 r_scbond_other 1.374 r_angle_refined_deg 1.372 r_angle_other_deg 1.343 r_mcbond_it 1.325 r_mcbond_other 1.323 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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 251 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling