2AGY

Crystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with tryptamine. Monoclinic form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6292PEG 2000 MME, ammonium sulphate, sodium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.446.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.703α = 90
b = 88.373β = 90.19
c = 79.709γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93ESRFID14-1

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
11.115920.06111.12.6357148-3
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)
11.11.14820.511.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.115357148189361000.1440.1440.1440.163RANDOM18.672
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]
-0.2-0.49-0.40.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.149
r_dihedral_angle_3_deg11.24
r_dihedral_angle_4_deg11.071
r_dihedral_angle_1_deg7.491
r_sphericity_free7.473
r_sphericity_bonded5.954
r_scangle_it3.458
r_scbond_it2.684
r_mcangle_it1.949
r_mcbond_it1.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.149
r_dihedral_angle_3_deg11.24
r_dihedral_angle_4_deg11.071
r_dihedral_angle_1_deg7.491
r_sphericity_free7.473
r_sphericity_bonded5.954
r_scangle_it3.458
r_scbond_it2.684
r_mcangle_it1.949
r_mcbond_it1.525
r_rigid_bond_restr1.398
r_angle_refined_deg1.29
r_mcbond_other1.052
r_angle_other_deg0.707
r_symmetry_vdw_other0.25
r_nbd_other0.206
r_nbd_refined0.205
r_symmetry_hbond_refined0.191
r_xyhbond_nbd_refined0.157
r_symmetry_vdw_refined0.156
r_xyhbond_nbd_other0.107
r_nbtor_other0.105
r_chiral_restr0.093
r_bond_refined_d0.013
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7245
Nucleic Acid Atoms
Solvent Atoms1512
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling