☰ Navigation Tabs
Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC57 and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JAZ LC51, 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,
0.1 M MES/imidazole pH6.5
0.02M amino amino acid
( 0.2M sodium L-glutamate, 0.2M DL-alanine, 0.2M glycine, 0.2M DL-lysine HCL, 0.2M DL serine)
Crystal Properties Matthews coefficient Solvent content 2.38 48.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.718 α = 104.13 b = 56.58 β = 103.33 c = 85.66 γ = 100.12
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) 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 41.37 97.8 0.095 0.095 7.4 3.6 95608 13.8
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 96.6 0.602 3.7
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 MOLECULAR REPLACEMENT THROUGHOUT LC51, 5JAZ 1.7 35 90831 4761 97.79 0.17955 0.17806 0.20824 0.2116 RANDOM 20.914
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] -0.51 -0.47 0.06 0.56 -1.3 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.624 r_dihedral_angle_4_deg 13.54 r_dihedral_angle_3_deg 13.023 r_dihedral_angle_1_deg 5.502 r_long_range_B_refined 4.467 r_long_range_B_other 4.303 r_scangle_other 2.184 r_mcangle_it 1.818 r_mcangle_other 1.818 r_scbond_it 1.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.624 r_dihedral_angle_4_deg 13.54 r_dihedral_angle_3_deg 13.023 r_dihedral_angle_1_deg 5.502 r_long_range_B_refined 4.467 r_long_range_B_other 4.303 r_scangle_other 2.184 r_mcangle_it 1.818 r_mcangle_other 1.818 r_scbond_it 1.299 r_scbond_other 1.298 r_angle_refined_deg 1.203 r_mcbond_it 1.057 r_mcbond_other 1.054 r_angle_other_deg 0.883 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 517 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling O model building