3KU9 | pdb_00003ku9

X-ray structure of the mutant lys300met of polyamine oxidase from zea mays in complex with spermine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KPF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.629350% SATURATED AMMONIUM SULFATE SOLUTION, 0.1M SODIUM ACETATE PH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.8574.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.957α = 90
b = 138.957β = 90
c = 189.8γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCD2009-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.2501000.1929.35.635410
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.23.271000.5573.25.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KPF3.25033582177099.80.1850.1830.190.2190.22RANDOM24.84
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]
1.570.781.57-2.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.876
r_dihedral_angle_3_deg20.591
r_dihedral_angle_4_deg16.245
r_dihedral_angle_1_deg10.15
r_scangle_it1.964
r_angle_refined_deg1.253
r_scbond_it1.122
r_mcangle_it0.775
r_mcbond_it0.395
r_chiral_restr0.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.876
r_dihedral_angle_3_deg20.591
r_dihedral_angle_4_deg16.245
r_dihedral_angle_1_deg10.15
r_scangle_it1.964
r_angle_refined_deg1.253
r_scbond_it1.122
r_mcangle_it0.775
r_mcbond_it0.395
r_chiral_restr0.081
r_bond_refined_d0.01
r_gen_planes_refined0.004
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7480
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms182

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling