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Crystal Structure of Plasmodium Falciparum Spermidine Synthase in Complex with METHYLTHIOADENOSIN AND SPERMIDINE after catalysis in crystal
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 AMMONIUM SULPHATE
Crystal Properties Matthews coefficient Solvent content 3.38 63.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.9 α = 90 b = 134.4 β = 95.5 c = 48.3 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 65 MM MULTILAYER MIRROR 2013-12-13 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 1.75 50 98.6 0.05 14.98 2.7 124715 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 1.75 1.86 98.7 0.53 2.29 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 1.75 44.94 118415 6255 98.57 0.18083 0.17902 0.1871 0.21554 0.2215 RANDOM 25.319
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 39.62 r_dihedral_angle_4_deg 19.121 r_dihedral_angle_3_deg 14.258 r_dihedral_angle_1_deg 6.607 r_angle_refined_deg 2.18 r_angle_other_deg 1.078 r_chiral_restr 0.149 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.62 r_dihedral_angle_4_deg 19.121 r_dihedral_angle_3_deg 14.258 r_dihedral_angle_1_deg 6.607 r_angle_refined_deg 2.18 r_angle_other_deg 1.078 r_chiral_restr 0.149 r_bond_refined_d 0.023 r_gen_planes_refined 0.012 r_bond_other_d 0.001 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 6750 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling MOLREP phasing