3MEN

Crystal structure of acetylpolyamine aminohydrolase from Burkholderia pseudomallei, iodide soak


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.3290EBS Wizard screen B1: 1.26M ammonium sulphate, 100mM cacodylate pH 6.5; protein at 7.9mg/ml; 1h soak in 1.4M ammonium sulphate, 100mM cacodylate pH 6.5, 200mM NaI, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.1442.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.7α = 90
b = 162.12β = 90
c = 173.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944VariMax2010-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.25098.10.10220.112.86653865263-332.72
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)
12.22.26840.4843.86.44850

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 DIFFRACTIONSADTHROUGHOUT2.2506653865263331598.10.1820.1790.237RANDOM23.25
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]
3.67-1.96-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.44
r_dihedral_angle_4_deg19.393
r_dihedral_angle_3_deg14.026
r_dihedral_angle_1_deg6.279
r_scangle_it3.245
r_scbond_it2.086
r_angle_refined_deg1.449
r_mcangle_it1.2
r_angle_other_deg0.969
r_mcbond_it0.673
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.44
r_dihedral_angle_4_deg19.393
r_dihedral_angle_3_deg14.026
r_dihedral_angle_1_deg6.279
r_scangle_it3.245
r_scbond_it2.086
r_angle_refined_deg1.449
r_mcangle_it1.2
r_angle_other_deg0.969
r_mcbond_it0.673
r_mcbond_other0.17
r_chiral_restr0.088
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10236
Nucleic Acid Atoms
Solvent Atoms516
Heterogen Atoms73

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling