4JIP

Crystal structure of glycerol trinitrate reductase NerA from Agrobacterium radiobacter in complex with 4-hydroxybenzaldehyde

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6	293	0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% w/v polyethylene glycol 3,350, pH 6.0, Microbatch, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.91	α = 90
b = 68.28	β = 90
c = 90.06	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		2010-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.29	54.41	97.9			17038	16687

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	2.29	2.41	93.1		0.309	3.6	3.6	2252

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	PDB entry 4jic	2.29	45.03	1.36	17038	16644	839	97.7	0.1965	0.1943	0.2387	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]
10.44			-2.3405		-6.5701

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.333
f_angle_d	0.934
f_chiral_restr	0.066
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2799
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms	40

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	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 R01GM133198.