☰ Navigation Tabs
Structure of Plasmodium falciparum DXR in complex with a beta-substituted fosmidomycin analogue, RC137, 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 6.5 293 10% w/v PEG 20,000, 20% v/v PEG MME 5502, 0.02M each of D-glucose, D- mannose, D-galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine, 0.1 M mes/imidazole pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.28 46.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.399 α = 89.64 b = 54.852 β = 105.4 c = 85.208 γ = 107.61
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 47.08 95.5 0.148 9.2 5.5 64132
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 0.798 2 5.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Y67 1.9 47.08 60876 3256 95.48 0.18904 0.18748 0.1935 0.21789 0.2238 RANDOM 29.577
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] -1.82 2.07 -0.5 3.07 0.52 -2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.525 r_dihedral_angle_4_deg 23.428 r_dihedral_angle_3_deg 16.721 r_dihedral_angle_1_deg 5.4 r_long_range_B_refined 4.722 r_long_range_B_other 4.645 r_scangle_other 2.987 r_mcangle_it 2.203 r_mcangle_other 2.203 r_scbond_it 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.525 r_dihedral_angle_4_deg 23.428 r_dihedral_angle_3_deg 16.721 r_dihedral_angle_1_deg 5.4 r_long_range_B_refined 4.722 r_long_range_B_other 4.645 r_scangle_other 2.987 r_mcangle_it 2.203 r_mcangle_other 2.203 r_scbond_it 1.779 r_scbond_other 1.765 r_angle_refined_deg 1.364 r_mcbond_it 1.341 r_mcbond_other 1.34 r_angle_other_deg 1.23 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.005 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 454 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling