2AGX | pdb_00002agx

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)
Type	Source	Accession Code	Details
experimental model	PDB	2AGY	substrate-free AADH coordinates

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	292	PEG 2000 MME, ammonium sulphate, sodium cacodylate, tryptamine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.7

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	30	91	0.1	12.6	4.7		49153		-3	25.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.2	2.28	75		0.332	28

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	substrate-free AADH coordinates	2.2	15	49011	2487	91.3	0.162	0.162	0.159	0.1651	0.225	0.2329	RANDOM	22.518

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			-0.47		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.189
r_dihedral_angle_4_deg	14.105
r_dihedral_angle_3_deg	13.992
r_dihedral_angle_1_deg	7.261
r_scangle_it	6.532
r_scbond_it	5.011
r_mcangle_it	3.081
r_mcbond_it	2.288
r_angle_refined_deg	1.309
r_nbd_refined	0.199

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.189
r_dihedral_angle_4_deg	14.105
r_dihedral_angle_3_deg	13.992
r_dihedral_angle_1_deg	7.261
r_scangle_it	6.532
r_scbond_it	5.011
r_mcangle_it	3.081
r_mcbond_it	2.288
r_angle_refined_deg	1.309
r_nbd_refined	0.199
r_symmetry_vdw_refined	0.185
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.14
r_chiral_restr	0.09
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7328
Nucleic Acid Atoms
Solvent Atoms	577
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.