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The structure of Plasmodium falciparum spermidine synthase in complex with 5'-methylthioadenosine and N-(3-aminopropyl)-trans-cyclohexane-1,4-diamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HTE PDB ENTRY 2HTE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 293 25% PEG 3350, 0.1M ammonium sulfate, 0.1M 2-(N-morpholino) ethanesulfonic acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.32 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.8 α = 90 b = 134.59 β = 94.55 c = 48.46 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 MULTILAYER MIRROR 2010-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 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 1.9 20 99.8 0.096 18.47 4.2 98147 -3 32.1
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 1.95 100 0.522 3.92 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2HTE 1.9 20 98147 93239 97.8 0.18 0.178 0.1824 0.1807 RANDOM 25.46
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] 1.65 -1.67 -1.7 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.768 r_angle_refined_deg 2.1 r_bond_refined_d 0.029 r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_gen_planes_other r_nbd_refined r_nbd_other
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.768 r_angle_refined_deg 2.1 r_bond_refined_d 0.029 r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 6745 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement CNS refinement XSCALE data scaling PDB_EXTRACT data extraction CNS phasing