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The structure of Plasmodium falciparum spermidine synthase in its apo-form
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 5.6 288 23% w/v PEG 3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.88 57.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 195.63 α = 90 b = 134.18 β = 94.07 c = 48.42 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 IMAGE PLATE MAR scanner 345 mm plate mirrors 2006-11-28 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 2.2 20 94.3 0.78 0.14 11.59 2.26 134273 59477 -3 37.145
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 2.256 93 0.264 0.351 5.4 2.24 35395
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 19.75 2 2 59477 58292 3068 94.3 0.20721 0.20721 0.20511 0.2087 0.24728 0.2502 RANDOM 37.145
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] 1.73 -3.32 -3.64 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_4_deg 22.802 r_dihedral_angle_3_deg 16.131 r_dihedral_angle_1_deg 6.48 r_scangle_it 2.845 r_scbond_it 1.863 r_angle_refined_deg 1.366 r_mcangle_it 1.353 r_mcbond_it 0.776 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.889 r_dihedral_angle_4_deg 22.802 r_dihedral_angle_3_deg 16.131 r_dihedral_angle_1_deg 6.48 r_scangle_it 2.845 r_scbond_it 1.863 r_angle_refined_deg 1.366 r_mcangle_it 1.353 r_mcbond_it 0.776 r_nbtor_refined 0.307 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.159 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.098 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 6480 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 57
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection XDS data reduction XSCALE data scaling PHASER phasing