3NYF

Crystal Structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase in Complex with Imino-Histidine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	277	0.1M 2-(N-morpholino)-ethanesulfonic acid (MES) pH 6.5-7.0, 5% glycerol, 6-10% (w/v) PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.101	α = 90
b = 78.148	β = 90
c = 89.593	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	CCD	MARMOSAIC 225 mm CCD		2009-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00000	APS	22-BM

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	1.3	50	90.4	0.049	3.2	6.5	97110	97110

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)
	1.3	1.35	54.7		0.306	3.2	2.7	5814

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	FREE R	PDB entry 3NYC	1.3	10	96756	96756	4838	90.2	0.1461	0.1444	0.177	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
11		3330.3

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.073
s_zero_chiral_vol	0.067
s_similar_adp_cmpnt	0.053
s_angle_d	0.03
s_from_restr_planes	0.0286
s_anti_bump_dis_restr	0.025
s_bond_d	0.012
s_rigid_bond_adp_cmpnt	0.005
s_similar_dist
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2916
Nucleic Acid Atoms
Solvent Atoms	353
Heterogen Atoms	64

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.