3VLX | pdb_00003vlx

Assimilatory nitrite reductase (Nii3) - N226K mutant - ligand free form from tobacco leaf

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.498	α = 90
b = 133.498	β = 90
c = 77.77	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	Rh coated collimating and focusing Si mirror	2010-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

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	1.35	50	100	0.08	8	14.3	152951	152951			18.2

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	1.35	1.4	100		0.468	4.68	13.8	15084

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	PDB ENTRY 3B0G	1.35	47.19	152899	152899	7671	100	0.1649	0.1649	0.1644	0.16	0.1748	0.17	RANDOM	14.7481

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			0.07		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.259
r_dihedral_angle_4_deg	12.354
r_dihedral_angle_3_deg	11.763
r_dihedral_angle_1_deg	5.982
r_scangle_it	2.507
r_scbond_it	1.536
r_angle_refined_deg	1.227
r_mcangle_it	0.926
r_mcbond_it	0.463
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.259
r_dihedral_angle_4_deg	12.354
r_dihedral_angle_3_deg	11.763
r_dihedral_angle_1_deg	5.982
r_scangle_it	2.507
r_scbond_it	1.536
r_angle_refined_deg	1.227
r_mcangle_it	0.926
r_mcbond_it	0.463
r_nbtor_refined	0.303
r_nbd_refined	0.199
r_metal_ion_refined	0.182
r_symmetry_hbond_refined	0.135
r_symmetry_vdw_refined	0.13
r_xyhbond_nbd_refined	0.101
r_chiral_restr	0.083
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4248
Nucleic Acid Atoms
Solvent Atoms	918
Heterogen Atoms	75

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.