2VR0

Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J7A	PDB ENTRY 2J7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	277	277 K 9% PEG 4K 0.1 M HEPES PH 7.5 100 MM GLYCYL-GLYCYL-GLYCINE VAPOUR DIFFUSION METHOD.

Crystal Properties
Matthews coefficient	Solvent content
3.5	65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.102	α = 90
b = 189.115	β = 90
c = 263.46	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	ADSC CCD		2006-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.8	29.77	86.5	0.11	9.4	2.8		92571		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	2.8	2.9	75.4		0.38	2.5	2.5

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	PDB ENTRY 2J7A	2.8	154.3	83976	2592	87	0.221	0.22	0.261	RANDOM	24.61

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]
-2.5			0.88		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.599
r_dihedral_angle_4_deg	18.826
r_dihedral_angle_3_deg	18.013
r_dihedral_angle_1_deg	5.878
r_scangle_it	1.506
r_angle_refined_deg	1.421
r_scbond_it	0.961
r_mcangle_it	0.508
r_nbtor_refined	0.305
r_mcbond_it	0.301
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.265
r_xyhbond_nbd_refined	0.141
r_metal_ion_refined	0.137
r_chiral_restr	0.094
r_symmetry_hbond_refined	0.056
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
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_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	18217
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	1250

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing