3VM0 | pdb_00003vm0

Assimilatory nitrite reductase (Nii3) - N226K mutant - NO2 complex from tobacco leaf

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
2.63	53.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.229	α = 90
b = 133.229	β = 90
c = 77.644	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 210r	Rh coated collimating and focusing Si mirror	2010-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	1.695	50	98.4	0.063	11.6	12	76165	76165			26.4

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	1.695	1.76	94.7		0.506	5.24	11.1	7216

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3B0G	1.695	26.76	75977	75977	3819	100	0.1642	0.163	0.16	0.1857	0.18	RANDOM	21.0945

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]
0.38			0.38		-0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.479
r_dihedral_angle_4_deg	12.431
r_dihedral_angle_3_deg	12.277
r_dihedral_angle_1_deg	6.021
r_scangle_it	3.385
r_scbond_it	2.075
r_angle_refined_deg	1.297
r_mcangle_it	1.169
r_mcbond_it	0.617
r_metal_ion_refined	0.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.479
r_dihedral_angle_4_deg	12.431
r_dihedral_angle_3_deg	12.277
r_dihedral_angle_1_deg	6.021
r_scangle_it	3.385
r_scbond_it	2.075
r_angle_refined_deg	1.297
r_mcangle_it	1.169
r_mcbond_it	0.617
r_metal_ion_refined	0.373
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4248
Nucleic Acid Atoms
Solvent Atoms	758
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.