8QQ7 | pdb_00008qq7

Structure of SpNOX: a Bacterial NADPH oxidase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	ITasser
experimental model	PDB	8QQ5	Seperate search of TM domain, manually edited from 5o0t, and DH domain solved by Xray structure.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein: 4.04 mg/ml in 50 mM Tris pH 7, 300 mM NaCl, 0.025 mM MNG3, 0.01 mM FAD. Crystallization condition: 30.5% PEG 300, 0.15 M Li2SO4, 0.15 M NaCl and 0.1 M MES pH6. Drop: 6 uL of protein + 6 uL of well.

Crystal Properties
Matthews coefficient	Solvent content
5.11	75.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 145.967	α = 90
b = 145.967	β = 90
c = 153.619	γ = 120

Symmetry
Space Group	P 64 2 2

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 2M		2018-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	3.62	47.82	90.9	0.072	0.074	0.017	19.6	20		5508

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.62	3.95	85.4		2	0.465	1.5	20

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	model from PROMALS3D and I-TASSER	3.62	47.82	5262	245	47.85	0.2642	0.26152	0.33	0.32003	0.33	RANDOM	201.602

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]
1.73	0.86		1.73		-5.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.378
r_mcangle_it	31.664
r_scbond_it	23.462
r_mcbond_it	19.415
r_dihedral_angle_4_deg	19.245
r_dihedral_angle_3_deg	17.803
r_dihedral_angle_1_deg	8.416
r_angle_refined_deg	1.727
r_chiral_restr	0.135
r_gen_planes_refined	0.008
r_bond_refined_d	0.006
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_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	3404
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building
PDB_EXTRACT	data extraction