2Z1Z

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana complexed with L-malate ion

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Native LL-diaminopimelate aminotransferase structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2.1M D,L-malic acid, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.587	α = 90
b = 102.587	β = 90
c = 172.939	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 210	KOHZU: Double Crystal Si(111)	2006-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11590	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	2.4	20	90.4	0.083	13.5	4	37831	37831

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	2.4	2.49	93.6		0.553	1.9	3.7	3838

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	Native LL-diaminopimelate aminotransferase structure	2.4	20	35896	35896	1916	90.16	0.18309	0.17956	0.25073	RANDOM	36.565

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]
-1.16	-0.58		-1.16		1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.465
r_dihedral_angle_4_deg	21.553
r_dihedral_angle_3_deg	21.136
r_dihedral_angle_1_deg	8.548
r_scangle_it	4.824
r_scbond_it	3.33
r_angle_refined_deg	2.374
r_mcangle_it	2.08
r_mcbond_it	1.259
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.465
r_dihedral_angle_4_deg	21.553
r_dihedral_angle_3_deg	21.136
r_dihedral_angle_1_deg	8.548
r_scangle_it	4.824
r_scbond_it	3.33
r_angle_refined_deg	2.374
r_mcangle_it	2.08
r_mcbond_it	1.259
r_nbtor_refined	0.318
r_symmetry_hbond_refined	0.271
r_nbd_refined	0.245
r_symmetry_vdw_refined	0.233
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.173
r_bond_refined_d	0.028
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6288
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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.