2ZOO

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

X-RAY DIFFRACTION

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 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.