3VM1

assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 complex from tobacco leaf

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	277	PEG4000, Tris-HCl, MgCl2, MPD, NaHCO3, pH 8.5, vapor diffusion, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.616	α = 90
b = 133.616	β = 90
c = 77.742	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	1.5	50	98.8	0.093	6.9	11.8	110538	110538			20.4

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	1.5	1.55	97.1		0.45	3.83	10.7	10692

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3B0G	1.5	35.94	110392	110392	5519	100	0.1637	0.1629	0.1788	RANDOM	15.0942

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]
-0.14			-0.14		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.993
r_dihedral_angle_4_deg	12.859
r_dihedral_angle_3_deg	11.786
r_dihedral_angle_1_deg	5.979
r_scangle_it	2.838
r_scbond_it	1.724
r_angle_refined_deg	1.254
r_mcangle_it	0.987
r_mcbond_it	0.511
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.993
r_dihedral_angle_4_deg	12.859
r_dihedral_angle_3_deg	11.786
r_dihedral_angle_1_deg	5.979
r_scangle_it	2.838
r_scbond_it	1.724
r_angle_refined_deg	1.254
r_mcangle_it	0.987
r_mcbond_it	0.511
r_nbtor_refined	0.305
r_nbd_refined	0.205
r_metal_ion_refined	0.195
r_symmetry_hbond_refined	0.166
r_symmetry_vdw_refined	0.138
r_xyhbond_nbd_refined	0.127
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	4248
Nucleic Acid Atoms
Solvent Atoms	924
Heterogen Atoms	78

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.