4YSQ

Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 8.38 MGy

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	0.1M sodium acetate, 5.5%(w/v) PEG 4000, 0.075M CuSO4

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.951	α = 90
b = 114.951	β = 90
c = 84.225	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	RAYONIX MX225HE		2014-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	0.75000	SPring-8	BL32XU

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	1.5	50	96.6	11.2	2.9		64868

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	1.5	34.35	61582	3286	96.49	0.14266	0.14029	0.14	0.18732	0.19	RANDOM	18.561

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		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.511
r_sphericity_free	36.63
r_dihedral_angle_3_deg	12.397
r_sphericity_bonded	10.512
r_dihedral_angle_1_deg	8.099
r_dihedral_angle_4_deg	6.597
r_long_range_B_refined	5.107
r_rigid_bond_restr	5.068
r_long_range_B_other	4.469
r_scangle_other	4.082
r_scbond_it	3.888
r_scbond_other	3.778
r_mcangle_other	2.882
r_mcangle_it	2.874
r_mcbond_it	2.444
r_mcbond_other	2.342
r_angle_refined_deg	1.908
r_angle_other_deg	0.901
r_chiral_restr	0.131
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2293
Nucleic Acid Atoms
Solvent Atoms	320
Heterogen Atoms	20

Software

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