2Z20 | pdb_00002z20

Crystal structure of LL-Diaminopimelate Aminotransferase from Arabidopsis thaliana

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	45% (NH4)2SO4, 0.1M HEPES pH7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.909	α = 90
b = 102.909	β = 90
c = 171.452	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	Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing)	2006-11-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.9793, 0.9795, 0.9185	SSRL	BL9-2

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	1.95	20	93.6	0.094	15.4	6.2	72271	72271

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	1.95	2.02	94.4		0.664	2.3	5.3	7204

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	MAD	THROUGHOUT	1.95	20	68601	68601	3658	93.5	0.18387	0.18154	0.1826	0.22713	0.2237	RANDOM	21.745

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]
-0.49	-0.24		-0.49		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.032
r_dihedral_angle_4_deg	22.193
r_dihedral_angle_3_deg	16.902
r_dihedral_angle_1_deg	7.188
r_scangle_it	4.26
r_scbond_it	2.984
r_angle_refined_deg	1.679
r_mcangle_it	1.605
r_mcbond_it	1.189
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.032
r_dihedral_angle_4_deg	22.193
r_dihedral_angle_3_deg	16.902
r_dihedral_angle_1_deg	7.188
r_scangle_it	4.26
r_scbond_it	2.984
r_angle_refined_deg	1.679
r_mcangle_it	1.605
r_mcbond_it	1.189
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.204
r_chiral_restr	0.196
r_xyhbond_nbd_refined	0.152
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6338
Nucleic Acid Atoms
Solvent Atoms	633
Heterogen Atoms	64

Software

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