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Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC177, and manganese
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Y67
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M MgCl2, 0.03M CaCl2, 0.1M MOPS/Hepes-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.384 α = 103.18 b = 55.759 β = 102.83 c = 85.433 γ = 100.91
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 2014-11-27 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 1.9 48.47 95.2 0.095 9.8 3.9 65358
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 1.9 2 95 0.542 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 4Y67 1.9 48.47 62042 3312 95.23 0.16655 0.16498 0.1723 0.19615 0.1994 RANDOM 21.648
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] -0.86 0.16 -0.58 1.31 -1.17 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.814 r_dihedral_angle_4_deg 26.57 r_dihedral_angle_3_deg 16.432 r_dihedral_angle_1_deg 5.485 r_long_range_B_refined 4.991 r_long_range_B_other 4.766 r_scangle_other 2.654 r_mcangle_it 1.944 r_mcangle_other 1.944 r_scbond_it 1.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.814 r_dihedral_angle_4_deg 26.57 r_dihedral_angle_3_deg 16.432 r_dihedral_angle_1_deg 5.485 r_long_range_B_refined 4.991 r_long_range_B_other 4.766 r_scangle_other 2.654 r_mcangle_it 1.944 r_mcangle_other 1.944 r_scbond_it 1.581 r_scbond_other 1.576 r_angle_refined_deg 1.376 r_mcbond_it 1.159 r_mcbond_other 1.159 r_angle_other_deg 1.035 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 573 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling