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Structure of Plasmodium Falciparum Spermidine Synthase in Complex with 1H-Benzimidazole-2-pentanamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I7C PDB ENTRY 2I7C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 27 % PEG 3350, 0.1 M MES PH 5.5, 0.1 M AMMONIUMSULPHATE
Crystal Properties Matthews coefficient Solvent content 3.34 63.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.498 α = 90 b = 134.38 β = 94.53 c = 48.277 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 110 CCD MARRESEARCH 165 MM MULTILAYER MIRROR 2012-09-28 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 1.83 30 97.9 0.08 12.85 3.13 108674 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 1.83 1.94 94.2 0.46 2.96 3.04
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 PDB ENTRY 2I7C 2.02 26.63 76694 4037 98.41 0.20693 0.20513 0.2105 0.24102 0.2411 RANDOM 23.96
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.102 r_dihedral_angle_4_deg 21.357 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 6.69 r_angle_refined_deg 1.935 r_angle_other_deg 0.902 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.102 r_dihedral_angle_4_deg 21.357 r_dihedral_angle_3_deg 15.157 r_dihedral_angle_1_deg 6.69 r_angle_refined_deg 1.935 r_angle_other_deg 0.902 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6649 Nucleic Acid Atoms Solvent Atoms 352 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing