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The structure of Plasmodium falciparum spermidine synthase in complex with decarboxylated S-adenosylmethionine
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, 2.5 mM dcAdoMet, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.89 57.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.3 α = 90 b = 134.18 β = 94.38 c = 48.32 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 2006-12-06 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) 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 2 20 96.1 0.72 0.115 13.67 3.22 80780 2 2 30.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.051 100 0.269 29.3 5.25 3.22 38389
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 (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 19.99 79372 4178 100 0.18217 0.18217 0.18048 0.1884 0.21407 0.2171 RANDOM 30.935
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] 1.85 -2.02 -2.22 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.799 r_dihedral_angle_4_deg 17.677 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 6.098 r_scangle_it 3.125 r_scbond_it 2.006 r_mcangle_it 1.358 r_angle_refined_deg 1.302 r_mcbond_it 0.823 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.799 r_dihedral_angle_4_deg 17.677 r_dihedral_angle_3_deg 14.351 r_dihedral_angle_1_deg 6.098 r_scangle_it 3.125 r_scbond_it 2.006 r_mcangle_it 1.358 r_angle_refined_deg 1.302 r_mcbond_it 0.823 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.266 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.201 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.091 r_bond_refined_d 0.012 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 6753 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement REFMAC refinement REFMAC refinement REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling PHASER phasing