5I5J

Shewanella denitrificans nitrous oxide reductase, reduced apo form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	25% PEG 3350 0.2 M lithium sulphate 0.1 M Tris/HCl

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.101	α = 90
b = 121.459	β = 90
c = 172.4	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2015-07-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.55	172.4	100	0.996	10.8	12.5		40073

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	5i5i	2.55	99.29	38052	1964	99.99	0.18962	0.18772	0.2278	RANDOM	38.803

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]
-3.38			0.33		3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.623
r_dihedral_angle_4_deg	19.025
r_dihedral_angle_3_deg	14.304
r_dihedral_angle_1_deg	6.937
r_long_range_B_refined	5.018
r_long_range_B_other	5.012
r_scangle_other	3.048
r_mcangle_it	2.599
r_mcangle_other	2.599
r_scbond_it	1.764
r_scbond_other	1.764
r_mcbond_it	1.503
r_mcbond_other	1.503
r_angle_refined_deg	1.427
r_angle_other_deg	1.03
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8343
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing