8AIE

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense complexed with D-cycloserine

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	0.2M NaNitrate, 0.1M Bis-tris propane pH 6,5, 20% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.968	α = 90
b = 90.028	β = 90
c = 100.29	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	PIXEL	RIGAKU HyPix-6000HE		2022-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54184

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	1.9	21.15	98.9	0.169	0.178	0.057	0.995	13.9	9.5		44377

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	1.9	1.94	94.7		3.483	3.715	1.258	0.417		7.9

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	1.9	21.15	41909	2191	98.13	0.2212	0.219	0.2642	RANDOM	30.653

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]
-0.41					0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.167
r_dihedral_angle_3_deg	15.906
r_dihedral_angle_4_deg	13.849
r_dihedral_angle_1_deg	7.198
r_angle_refined_deg	1.762
r_angle_other_deg	1.388
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.167
r_dihedral_angle_3_deg	15.906
r_dihedral_angle_4_deg	13.849
r_dihedral_angle_1_deg	7.198
r_angle_refined_deg	1.762
r_angle_other_deg	1.388
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4295
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms	77

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
CrysalisPro	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.