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Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 40 % PEG 4000, 6% PEG 20000, 0.1 M Tris-HCl, 0.1 M Potassium phosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.669 α = 90 b = 96.996 β = 106.33 c = 69.649 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315 2005-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.97000 ALS 8.2.2
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 2.5 20 87.5 0.07 0.081 12.23 3.3 16956 16956
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 2.5 2.6 53.6 0.396 0.381 3.2 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 SAD THROUGHOUT 2.5 20 16306 16306 895 89.11 0.20068 0.19796 0.2043 0.24785 0.2541 RANDOM 32.099
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] -1.08 0.19 0.57 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_3_deg 14.804 r_dihedral_angle_4_deg 14.612 r_dihedral_angle_1_deg 4.954 r_scangle_it 3.41 r_scbond_it 2.293 r_mcangle_it 1.835 r_mcbond_it 1.641 r_angle_refined_deg 1.058 r_angle_other_deg 0.862
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.519 r_dihedral_angle_3_deg 14.804 r_dihedral_angle_4_deg 14.612 r_dihedral_angle_1_deg 4.954 r_scangle_it 3.41 r_scbond_it 2.293 r_mcangle_it 1.835 r_mcbond_it 1.641 r_angle_refined_deg 1.058 r_angle_other_deg 0.862 r_mcbond_other 0.209 r_symmetry_hbond_refined 0.197 r_symmetry_vdw_other 0.196 r_nbd_refined 0.185 r_nbd_other 0.18 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.133 r_symmetry_vdw_refined 0.109 r_nbtor_other 0.08 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4500 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data reduction XSCALE data scaling SHELXD phasing