☰ Navigation Tabs
The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine and the inhibitor cis-4-methylcyclohexylamine (4MCHA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 288 25% PEG3350, 0.1 M Ammonium Sulphate and 0.1 M Bis-Tris pH5.5, 2.5 mM dcAdoMet, 2.5 mM 4MCHA, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.88 62.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.24 α = 90 b = 134.1 β = 94.53 c = 48.35 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm mirrors 2006-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.043 MAX II I911-2
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 2.2 20 98.8 0.086 9.85 3.45 62364 2 -3 39.247
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 2.2 2.5 98.8 0.346 3.8 3.45 19744
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2I7C 2.2 19.77 -3 2 60721 59243 3119 93.6 0.2 0.19831 0.19615 0.202 0.23883 0.247 RANDOM 35.374
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] 1.96 -2.75 -3.28 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_4_deg 21.646 r_dihedral_angle_3_deg 16.66 r_dihedral_angle_1_deg 6.382 r_scangle_it 3.157 r_scbond_it 1.963 r_angle_refined_deg 1.46 r_mcangle_it 1.339 r_mcbond_it 0.759 r_symmetry_vdw_refined 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.529 r_dihedral_angle_4_deg 21.646 r_dihedral_angle_3_deg 16.66 r_dihedral_angle_1_deg 6.382 r_scangle_it 3.157 r_scbond_it 1.963 r_angle_refined_deg 1.46 r_mcangle_it 1.339 r_mcbond_it 0.759 r_symmetry_vdw_refined 0.45 r_nbtor_refined 0.31 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6744 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling PHASER phasing