2AGX

Crystal structure of the Schiff base intermediate in the reductive half-reaction of aromatic amine dehydrogenase (AADH) with tryptamine. P212121 form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AGYsubstrate-free AADH coordinates

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6292PEG 2000 MME, ammonium sulphate, sodium cacodylate, tryptamine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.372α = 90
b = 96.194β = 90
c = 120.321γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8EMBL/DESY, HAMBURGX11

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
12.230910.112.64.749153-325.3
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)
2.22.28750.33228

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTsubstrate-free AADH coordinates2.21549011248791.30.1620.1620.1590.225RANDOM22.518
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]
0.43-0.470.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.189
r_dihedral_angle_4_deg14.105
r_dihedral_angle_3_deg13.992
r_dihedral_angle_1_deg7.261
r_scangle_it6.532
r_scbond_it5.011
r_mcangle_it3.081
r_mcbond_it2.288
r_angle_refined_deg1.309
r_nbd_refined0.199
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.189
r_dihedral_angle_4_deg14.105
r_dihedral_angle_3_deg13.992
r_dihedral_angle_1_deg7.261
r_scangle_it6.532
r_scbond_it5.011
r_mcangle_it3.081
r_mcbond_it2.288
r_angle_refined_deg1.309
r_nbd_refined0.199
r_symmetry_vdw_refined0.185
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.14
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7328
Nucleic Acid Atoms
Solvent Atoms577
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing