3GJY

Crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82890.2M Potassium sodium tartrate, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1342.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.909α = 90
b = 65.009β = 90
c = 87.308γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Mirror2008-11-23MSAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97915APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.472399.40.06843.58.25137151371
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.471.595.60.4822.886.62418

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.4722.624863948639261499.280.15880.15880.157040.19152RANDOM20.23
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]
-0.010.04-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.834
r_dihedral_angle_4_deg17.204
r_dihedral_angle_3_deg12.74
r_sphericity_free6.758
r_dihedral_angle_1_deg6.159
r_scangle_it4.535
r_sphericity_bonded4.15
r_scbond_it3.14
r_mcangle_it2.231
r_rigid_bond_restr1.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.834
r_dihedral_angle_4_deg17.204
r_dihedral_angle_3_deg12.74
r_sphericity_free6.758
r_dihedral_angle_1_deg6.159
r_scangle_it4.535
r_sphericity_bonded4.15
r_scbond_it3.14
r_mcangle_it2.231
r_rigid_bond_restr1.702
r_angle_refined_deg1.459
r_mcbond_it1.454
r_chiral_restr0.11
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2251
Nucleic Acid Atoms
Solvent Atoms388
Heterogen Atoms

Software

Software
Software NamePurpose
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing