3EI6

Crystal structure of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with PLP-DAP: an external aldimine mimic

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z20	PDB entry 2Z20

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	45% (NH4)2SO4, 0.1 M HEPES pH 7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.67	α = 90
b = 102.67	β = 90
c = 172.145	γ = 120

Symmetry
Space Group	P 32 2 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	ADSC QUANTUM 315		2007-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.115872	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	40	94.1	0.053			78472	78472

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	66.1		0.256

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB entry 2Z20	1.9	39.5	74474	74474	3938	94.03	0.15847	0.15684	0.18905	RANDOM	24.995

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]
-0.66	-0.33		-0.66		0.99

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.538
r_dihedral_angle_4_deg	19.997
r_dihedral_angle_3_deg	13.389
r_dihedral_angle_1_deg	5.654
r_scangle_it	3.815
r_scbond_it	2.43
r_mcangle_it	1.439
r_angle_refined_deg	1.328
r_mcbond_it	0.908
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.538
r_dihedral_angle_4_deg	19.997
r_dihedral_angle_3_deg	13.389
r_dihedral_angle_1_deg	5.654
r_scangle_it	3.815
r_scbond_it	2.43
r_mcangle_it	1.439
r_angle_refined_deg	1.328
r_mcbond_it	0.908
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.2
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6338
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	89

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.