2AKJ | pdb_00002akj

Structure of spinach nitrite reductase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	Tris HCl, polyethylene glycol 4000, MgCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.97	α = 90
b = 128.97	β = 90
c = 120.95	γ = 90

Symmetry
Space Group	P 41 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	110	IMAGE PLATE	RIGAKU RAXIS IV		2004-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.8	40	99.63	0.124	4.5	3.9	24304	24304

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.8	2.9	97.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SIRAS	THROUGHOUT	2.8	40	24304	24304	1300	99.63	0.25228	0.25228	0.24974	0.2507	0.30009	0.2436	RANDOM	38.143

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]
-2.65			-2.65		5.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.101
r_dihedral_angle_3_deg	22.913
r_dihedral_angle_4_deg	18.008
r_dihedral_angle_1_deg	6.721
r_scangle_it	2.186
r_angle_refined_deg	1.749
r_scbond_it	1.236
r_mcangle_it	0.884
r_mcbond_it	0.493
r_nbtor_refined	0.322
r_nbd_refined	0.25
r_symmetry_vdw_refined	0.235
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.123
r_symmetry_hbond_refined	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4222
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	71

Software

Software
Software Name	Purpose
CrystalClear	data collection
d*TREK	data reduction
SOLVE	phasing
REFMAC	refinement
CrystalClear	data reduction
d*TREK	data scaling