8AYJ

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiens complexed with 3-aminooxypropionic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AHR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	0.02 M Sodium/potassium phosphate,0.1 M Bis-Tris propane pH 6.5, 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.573	α = 90
b = 58.434	β = 94.11
c = 96.722	γ = 90

Symmetry
Space Group	P 1 21 1

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	MAR CCD 165 mm		2022-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	KURCHATOV SNC BEAMLINE K4.4	0.74503	KURCHATOV SNC	K4.4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.75	48.24	98.9	0.162	0.196	0.109	0.99	4.3	3		56226

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	95.4		1.124	1.363	0.761	0.425		2.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8AHR	1.75	48.24	53435	2774	98.87	0.2029	0.201	0.2393	RANDOM	14.988

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]
0.95		0.24	-0.96		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.558
r_dihedral_angle_4_deg	17.995
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_1_deg	7.386
r_angle_refined_deg	1.878
r_angle_other_deg	1.409
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.558
r_dihedral_angle_4_deg	17.995
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_1_deg	7.386
r_angle_refined_deg	1.878
r_angle_other_deg	1.409
r_chiral_restr	0.101
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4285
Nucleic Acid Atoms
Solvent Atoms	406
Heterogen Atoms	122

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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.