4YSA

Completely oxidized structure of copper nitrite reductase from Geobacillus thermodenitrificans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	5.5% PEG 4000, 0.1M sodium acetate pH 4.5, 0.075M copper sulphate

Crystal Properties
Matthews coefficient	Solvent content
3.13	60.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.197	α = 90
b = 116.197	β = 90
c = 85.553	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	293	CCD	MPCCD		2014-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SACLA BEAMLINE BL3	1.129	SACLA	BL3

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	1.43	34.8	100	3.4	245.3		79590

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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		THROUGHOUT	1.43	34.75	75525	4063	99.99	0.13734	0.1367	0.14	0.14915	0.15	RANDOM	23.983

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]
0.01	0.01		0.01		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.706
r_dihedral_angle_3_deg	14.863
r_sphericity_free	13.641
r_dihedral_angle_4_deg	12.058
r_rigid_bond_restr	7.988
r_dihedral_angle_1_deg	7.86
r_sphericity_bonded	6.595
r_scbond_it	2.877
r_angle_refined_deg	2.385
r_long_range_B_refined	2.014
r_mcangle_it	1.512
r_mcbond_it	1.459
r_chiral_restr	0.152
r_bond_refined_d	0.029
r_gen_planes_refined	0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2286
Nucleic Acid Atoms
Solvent Atoms	134
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
CrystFEL	data reduction