2OO0

A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5288.1525% PEG3350, 0.2 M ammonium acetate, O.1M MES, 2mM XAP, 0.3 % cadaverine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K
Crystal Properties
Matthews coefficientSolvent content
2.9257.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.018α = 90
b = 87.11β = 91.02
c = 130.08γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2006-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.929.4597.859293822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.94993.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1D7K1.929.452929388520394681000.187170.184220.21345RANDOM24.566
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]
-0.13-0.870.99-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.262
r_dihedral_angle_4_deg17.852
r_dihedral_angle_3_deg14.298
r_dihedral_angle_1_deg5.689
r_scangle_it2.692
r_scbond_it1.691
r_angle_refined_deg1.179
r_mcangle_it1.153
r_mcbond_it0.72
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.262
r_dihedral_angle_4_deg17.852
r_dihedral_angle_3_deg14.298
r_dihedral_angle_1_deg5.689
r_scangle_it2.692
r_scbond_it1.691
r_angle_refined_deg1.179
r_mcangle_it1.153
r_mcbond_it0.72
r_nbtor_refined0.305
r_symmetry_vdw_refined0.204
r_nbd_refined0.191
r_symmetry_hbond_refined0.174
r_xyhbond_nbd_refined0.127
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6559
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing