2ZOO

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1KBW	PDB ENTRY 1kbw, 1c52
experimental model	PDB	1C52	PDB ENTRY 1kbw, 1c52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	277	Lithium sulfate, Ammonium sulfate, Sodium citrate, Sucrose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.338	α = 90
b = 180.338	β = 90
c = 180.338	γ = 90

Symmetry
Space Group	P 41 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	Bruker DIP-6040		2007-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	43.8	99.1			72995	72995

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	99.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 1kbw, 1c52	1.95	8	63885	7167	99.21	0.16769	0.16564	0.18604	RANDOM	25.22

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.99
r_dihedral_angle_4_deg	18.419
r_dihedral_angle_3_deg	15.454
r_dihedral_angle_1_deg	6.96
r_scangle_it	3.643
r_scbond_it	2.334
r_angle_refined_deg	1.519
r_mcangle_it	1.365
r_mcbond_it	0.993
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.99
r_dihedral_angle_4_deg	18.419
r_dihedral_angle_3_deg	15.454
r_dihedral_angle_1_deg	6.96
r_scangle_it	3.643
r_scbond_it	2.334
r_angle_refined_deg	1.519
r_mcangle_it	1.365
r_mcbond_it	0.993
r_nbtor_refined	0.309
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.201
r_symmetry_vdw_refined	0.191
r_chiral_restr	0.127
r_xyhbond_nbd_refined	0.12
r_metal_ion_refined	0.065
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3326
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling

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 R01GM133198.