3VKQ | pdb_00003vkq

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3B0G

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
2.64	53.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.15	α = 90
b = 134.15	β = 90
c = 77.994	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 315r	Two dimensional focusing mirror	2011-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.9	SPring-8	BL38B1

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	1.6	50	99.5	0.077	0.077	9.1	13.2	93525	93525			20.2

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	1.6	1.66	97.8		0.396	6.93	12.8	9076

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3B0G	1.6	37.27	93474	93474	4690	100	0.153	0.153	0.1523	0.15	0.1678	0.17	RANDOM	15.0832

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]
0.04			0.04		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.008
r_dihedral_angle_4_deg	13.167
r_dihedral_angle_3_deg	11.805
r_dihedral_angle_1_deg	6.061
r_scangle_it	2.84
r_scbond_it	1.728
r_angle_refined_deg	1.25
r_mcangle_it	0.954
r_mcbond_it	0.493
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.008
r_dihedral_angle_4_deg	13.167
r_dihedral_angle_3_deg	11.805
r_dihedral_angle_1_deg	6.061
r_scangle_it	2.84
r_scbond_it	1.728
r_angle_refined_deg	1.25
r_mcangle_it	0.954
r_mcbond_it	0.493
r_nbtor_refined	0.306
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.166
r_symmetry_vdw_refined	0.155
r_metal_ion_refined	0.123
r_xyhbond_nbd_refined	0.108
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4246
Nucleic Acid Atoms
Solvent Atoms	1025
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 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 R01GM157729.