3H7C

Crystal Structure of Arabidopsis thaliana Agmatine Deiminase from Cell Free Expression

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	Protein solution- 10 mg/ml agmatine deiminase, 50 mM NaCl, 0.3 mM TCEP, 5 mM HEPES, pH 7.0; Precipitant solution- 34% Polyethylene glycol 2000, 200 mM KBr, 100 mM triethanolamine, pH 7.5; Cryoprotectant- MiTeGen LV Cryo Oil, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.715	α = 90
b = 69.932	β = 98.4
c = 50.917	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 300 mm CCD		2009-04-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.96350,0.97943,0.97957	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.5	50	100	0.098	19.6	7.5	68398	68398

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.53	100		0.444	4.1	6.7	3395

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.5	50	68375	3460	99.75	0.147	0.146	0.174	RANDOM	14.686

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		-0.37	0.65		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.777
r_dihedral_angle_4_deg	18.289
r_dihedral_angle_3_deg	13.184
r_dihedral_angle_1_deg	7.044
r_scangle_it	5.677
r_scbond_it	3.598
r_mcangle_it	2.519
r_angle_refined_deg	1.63
r_mcbond_it	1.541
r_chiral_restr	0.131

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.777
r_dihedral_angle_4_deg	18.289
r_dihedral_angle_3_deg	13.184
r_dihedral_angle_1_deg	7.044
r_scangle_it	5.677
r_scbond_it	3.598
r_mcangle_it	2.519
r_angle_refined_deg	1.63
r_mcbond_it	1.541
r_chiral_restr	0.131
r_gen_planes_refined	0.018
r_bond_refined_d	0.017

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3073
Nucleic Acid Atoms
Solvent Atoms	372
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.