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The crystal structure of spermidine synthase from p. falciparum in complex with 5'-methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZDZ PDB ENTRY 1ZDZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 291 25% w/v PEG3350, 0.1M Ammonium Sulphate, 0.1M Bis-Tris, 4 mM 5'-methylthioadenosine, pH 5.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.31 62.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 197.061 α = 90 b = 134.6 β = 94.66 c = 48.336 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 RIGAKU RAXIS IV 2006-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 97.8 0.108 15.8 3.8 84688 82781 1 1 28.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 81 0.877 1.48 3.6 3421
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 (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 PDB ENTRY 1ZDZ 2 33.08 79849 78619 4135 98.46 0.192 0.18782 0.1855 0.1834 0.23122 0.2279 RANDOM 28.989
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 38.526 r_dihedral_angle_4_deg 16.514 r_dihedral_angle_3_deg 15.498 r_dihedral_angle_1_deg 6.347 r_scangle_it 3.842 r_scbond_it 2.558 r_mcangle_it 1.695 r_angle_refined_deg 1.628 r_mcbond_it 1.058 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.526 r_dihedral_angle_4_deg 16.514 r_dihedral_angle_3_deg 15.498 r_dihedral_angle_1_deg 6.347 r_scangle_it 3.842 r_scbond_it 2.558 r_mcangle_it 1.695 r_angle_refined_deg 1.628 r_mcbond_it 1.058 r_nbtor_refined 0.305 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.169 r_symmetry_vdw_refined 0.152 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.121 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6616 Nucleic Acid Atoms Solvent Atoms 571 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing