☰ Navigation Tabs
Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, LC50 and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JAZ 5JAZ (LC51)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 12.5% W/V PEG 1000, 12.5% PEG 3350, 12.5% v/v MPD
0.03M of each ethylene glycol
0.1M MOPS/HEPES-Na pH 7.5
(0.3M diethyleneglycol, 0.3M triethyleneglycol, 0.3M tetraethyleneglycol, 0.3M pentaethyleneglycol)
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.43 α = 103.57 b = 56.193 β = 103.07 c = 86.046 γ = 100.4
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 PILATUS3 6M 2015-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979490 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 28.96 96.4 0.071 0.998 10.2 3.6 123676 13
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 1.55 1.58 87.9 0.49 1.7 3.3
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 (LC51) 1.55 28 117573 6099 96.35 0.18143 0.18036 0.1893 0.20204 0.2076 RANDOM 18.657
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] -0.19 0.2 -0.8 1.02 -0.42 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.113 r_dihedral_angle_4_deg 21.001 r_dihedral_angle_3_deg 12.547 r_dihedral_angle_1_deg 5.547 r_long_range_B_refined 3.828 r_long_range_B_other 3.626 r_scangle_other 1.71 r_mcangle_it 1.494 r_mcangle_other 1.494 r_angle_refined_deg 1.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.113 r_dihedral_angle_4_deg 21.001 r_dihedral_angle_3_deg 12.547 r_dihedral_angle_1_deg 5.547 r_long_range_B_refined 3.828 r_long_range_B_other 3.626 r_scangle_other 1.71 r_mcangle_it 1.494 r_mcangle_other 1.494 r_angle_refined_deg 1.176 r_scbond_it 1.017 r_scbond_other 1.017 r_angle_other_deg 0.867 r_mcbond_it 0.849 r_mcbond_other 0.849 r_chiral_restr 0.072 r_bond_refined_d 0.007 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 545 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling O model building