3VKP

Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with low X-ray dose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	PEG4000, Tris-HCl, MgCl2, MPD, NaNO2, pH 8.5, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.107	α = 90
b = 133.107	β = 90
c = 77.796	γ = 90

Symmetry
Space Group	P 4 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 270	Vertical and horizontal Silicon single crystal mirrors	2008-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.0	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.4	50	97.4	0.118	0.118	6.4	6.5	134915	134915			21.7

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	1.4	1.45	77.2		0.404	2.52	6	10563

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3B0G	1.4	29.25	134844	134844	6773	100	0.1757	0.1757	0.175	0.1892	RANDOM	16.8876

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]
-0.31			-0.31		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.399
r_dihedral_angle_4_deg	13.163
r_dihedral_angle_3_deg	11.86
r_dihedral_angle_1_deg	5.982
r_scangle_it	2.471
r_scbond_it	1.51
r_angle_refined_deg	1.217
r_mcangle_it	0.886
r_mcbond_it	0.455
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.399
r_dihedral_angle_4_deg	13.163
r_dihedral_angle_3_deg	11.86
r_dihedral_angle_1_deg	5.982
r_scangle_it	2.471
r_scbond_it	1.51
r_angle_refined_deg	1.217
r_mcangle_it	0.886
r_mcbond_it	0.455
r_nbtor_refined	0.306
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.144
r_symmetry_hbond_refined	0.118
r_metal_ion_refined	0.101
r_xyhbond_nbd_refined	0.096
r_chiral_restr	0.082
r_bond_refined_d	0.007
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4246
Nucleic Acid Atoms
Solvent Atoms	922
Heterogen Atoms	77

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction

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.