3WI9

Crystal structure of copper nitrite reductase from Geobacillus kaustophilus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	277	0.1M Acetate, 5.5% PEG4000, 175mM ZnSO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.069	α = 90
b = 115.069	β = 90
c = 87.505	γ = 120

Symmetry
Space Group	H 3

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	ADSC QUANTUM 210		2010-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	1.3	18.9	95.2	14.9	3.5	101119	101119	2	2

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	1.3	1.37	90.8		2.4	2.4

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	1kbw	1.3	18.9	96275	5038	95.09	0.1824	0.18162	0.19747	RANDOM	18.319

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]
-1.05	-0.53		-1.05		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.177
r_dihedral_angle_3_deg	10.657
r_dihedral_angle_4_deg	8.663
r_dihedral_angle_1_deg	7.402
r_sphericity_free	3.516
r_sphericity_bonded	2.834
r_scangle_it	2.767
r_scbond_it	1.89
r_angle_refined_deg	1.296
r_mcangle_it	1.175
r_rigid_bond_restr	0.925
r_mcbond_it	0.749
r_nbtor_refined	0.304
r_metal_ion_refined	0.266
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.192
r_symmetry_metal_ion_refined	0.167
r_xyhbond_nbd_refined	0.118
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.087
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2350
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	24

Software

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