3BWB

Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827740 % 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 coefficientSolvent content
2.0540

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.669α = 90
b = 96.996β = 106.33
c = 69.649γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152005-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.97000ALS8.2.2

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.52087.50.070.08112.233.31695616956
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)RedundancyNumber Unique Reflections (All)
12.52.653.60.3960.3813.22.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.520163061630689589.110.200680.197960.24785RANDOM32.099
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]
-1.080.190.570.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.519
r_dihedral_angle_3_deg14.804
r_dihedral_angle_4_deg14.612
r_dihedral_angle_1_deg4.954
r_scangle_it3.41
r_scbond_it2.293
r_mcangle_it1.835
r_mcbond_it1.641
r_angle_refined_deg1.058
r_angle_other_deg0.862
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.519
r_dihedral_angle_3_deg14.804
r_dihedral_angle_4_deg14.612
r_dihedral_angle_1_deg4.954
r_scangle_it3.41
r_scbond_it2.293
r_mcangle_it1.835
r_mcbond_it1.641
r_angle_refined_deg1.058
r_angle_other_deg0.862
r_mcbond_other0.209
r_symmetry_hbond_refined0.197
r_symmetry_vdw_other0.196
r_nbd_refined0.185
r_nbd_other0.18
r_nbtor_refined0.172
r_xyhbond_nbd_refined0.133
r_symmetry_vdw_refined0.109
r_nbtor_other0.08
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms4500
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
XDSdata reduction
XSCALEdata scaling
SHELXDphasing