2J7A

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	277	10% PEG 4K, 0.1 M HEPES PH 7.5, 30 MM GLYCYL-GLYCYL-GLYCINE

Crystal Properties
Matthews coefficient	Solvent content
3.6	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.664	α = 90
b = 258.117	β = 90
c = 580.742	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARRESEACH			M	MAD

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

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	2.3	53	83.9	0.1	8.3	2.9		443656		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	67.3		0.31	3.1	2.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.3	288.67	421309	22270	83.7	0.203	0.201	0.24	RANDOM	20.47

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]
-1.19			0.84		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.518
r_dihedral_angle_4_deg	21.827
r_dihedral_angle_3_deg	17.264
r_dihedral_angle_1_deg	6.479
r_scangle_it	2.519
r_scbond_it	1.636
r_angle_refined_deg	1.463
r_mcangle_it	1.084
r_mcbond_it	0.639
r_nbtor_refined	0.298
r_nbd_refined	0.254
r_symmetry_vdw_refined	0.228
r_symmetry_hbond_refined	0.186
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.103
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	54627
Nucleic Acid Atoms
Solvent Atoms	2325
Heterogen Atoms	3858

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing