8CAK

Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with M41

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	0.3 M diethylene glycol; 0.3 M triethylene glycol, 0.3 M tetraethylene glycol, 0.3 M pentaethylene glycol, Tris-HCl 0.1 M pH 8.0, 20% (v/v) ethylene glycol, 10% (w/v) PEG8000

Crystal Properties
Matthews coefficient	Solvent content
5.1	75.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.476	α = 90
b = 127.476	β = 90
c = 71.944	γ = 120

Symmetry
Space Group	P 3 2 1

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		2020-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	1.000002	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.67	47.76	99.6	0.198	0.207	0.061	0.997	11.4	11.3		19417

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.67	2.8	97		1.8	1	0.554	0.625		11.4

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.67	47.75	18444	971	99.65	0.2039	0.2017	0.2445	RANDOM	53.632

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]
0.05	0.03		0.05		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.02
r_dihedral_angle_4_deg	20.186
r_dihedral_angle_3_deg	17.884
r_dihedral_angle_1_deg	9.01
r_angle_refined_deg	1.935
r_angle_other_deg	1.4
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.02
r_dihedral_angle_4_deg	20.186
r_dihedral_angle_3_deg	17.884
r_dihedral_angle_1_deg	9.01
r_angle_refined_deg	1.935
r_angle_other_deg	1.4
r_chiral_restr	0.082
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2024
Nucleic Acid Atoms
Solvent Atoms	23
Heterogen Atoms	93

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.