3B0G | pdb_00003b0g

Assimilatory nitrite reductase (Nii3) from tobbaco leaf

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AKJ

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
2.63	53.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 134.051	α = 90
b = 134.051	β = 90
c = 77.801	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	100	CCD	Bruker DIP-6040	Rh-coated mirror	2007-11-20	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)	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	1.25	50	99.9	0.066		6.4	193657	193657

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	1.25	1.29	100		0.492		6.2	19171

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	2AKJ	1.25	33.54	199364	183633	9731	100	0.1608	0.1608	0.1604	0.1597	0.1685	0.1673	RANDOM	13.9735

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]
0.09			0.09		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.027
r_dihedral_angle_4_deg	12.471
r_dihedral_angle_3_deg	11.366
r_dihedral_angle_1_deg	5.976
r_scangle_it	2.377
r_scbond_it	1.466
r_angle_refined_deg	1.218
r_mcangle_it	0.89
r_mcbond_it	0.446
r_nbtor_refined	0.304
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.154
r_symmetry_vdw_refined	0.131
r_metal_ion_refined	0.121
r_xyhbond_nbd_refined	0.09
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	4246
Nucleic Acid Atoms
Solvent Atoms	924
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing