3B33

Crystal structure of the PAS domain of nitrogen regulation protein NR(II) from Vibrio parahaemolyticus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	289	0.1 M Sodium acetate, 3 M Sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.115	α = 90
b = 81.115	β = 90
c = 67.467	γ = 120

Symmetry
Space Group	P 63 2 2

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		2007-10-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97920	APS	19-ID

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	1.83	35.12	98.8	0.072	11.3	18.3	11960	11960			40.5

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	1.83	1.88	88.8		0.61	2.18	6.1	872

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.83	35.12	11938	11938	566	98.77	0.1843	0.1843	0.1837	0.1958	RANDOM	33.354

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]
0.07	0.03		0.07		-0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.231
r_dihedral_angle_4_deg	19.435
r_dihedral_angle_3_deg	17.216
r_dihedral_angle_1_deg	6.496
r_scangle_it	3.449
r_scbond_it	2.279
r_mcangle_it	1.974
r_angle_refined_deg	1.78
r_mcbond_it	1.194
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.231
r_dihedral_angle_4_deg	19.435
r_dihedral_angle_3_deg	17.216
r_dihedral_angle_1_deg	6.496
r_scangle_it	3.449
r_scbond_it	2.279
r_mcangle_it	1.974
r_angle_refined_deg	1.78
r_mcbond_it	1.194
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.29
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.193
r_chiral_restr	0.136
r_symmetry_hbond_refined	0.101
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	838
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	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.