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Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PWP PDB entry 2PWP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 291 25% w/v PEG 3350, 0.1M Ammonium sulfate, 0.1M Bis-tris, pH 5.5, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.34 63.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.483 α = 90 b = 134.584 β = 96.36 c = 48.37 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 Mirrors 2007-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 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 30 98.5 0.068 16.67 3.4 84798 84798 32.4
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 2.07 90.8 0.472 2.21 3.2 7768
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 2PWP 2 29.44 80454 4239 98.83 0.21634 0.21458 0.2065 0.24978 0.2415 RANDOM 35.564
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] 0.09 -0.06 -0.05 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.081 r_dihedral_angle_4_deg 22.62 r_dihedral_angle_3_deg 14.082 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.511 r_scbond_it 1.657 r_angle_refined_deg 1.325 r_mcangle_it 1.124 r_mcbond_it 0.662 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.081 r_dihedral_angle_4_deg 22.62 r_dihedral_angle_3_deg 14.082 r_dihedral_angle_1_deg 6.343 r_scangle_it 2.511 r_scbond_it 1.657 r_angle_refined_deg 1.325 r_mcangle_it 1.124 r_mcbond_it 0.662 r_nbtor_refined 0.304 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.131 r_symmetry_hbond_refined 0.099 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6753 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 102
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing