8CAO | pdb_00008cao

Crystal structure of dehydrogenase domain of Cylindrospermum stagnale NADPH-Oxidase 5 (NOX5) in complex with CA24

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	5O0X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	293	MES 0.1 mM pH 6.5, 0.1 M carboxylic acids, 20% v/v ethylene glycol, 10% w/v PEG8000

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 127.428	α = 90
b = 127.428	β = 90
c = 71.992	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		2021-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	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	2.3	47.76	99.7	0.203	0.231	0.106	0.964	4.2	4.2		30148

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	2.3	2.38	99.7		1.176	1.342	0.627	0.448		4.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	47.76	28597	1530	99.55	0.217	0.2164	0.22	0.2264	0.23	RANDOM	56.8627

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]
1.18	0.59		1.18		-3.84

RMS Deviations
Key	Refinement Restraint Deviation
TORSION ANGLES. PERIOD 2 (DEGREES)	34.59
TORSION ANGLES. PERIOD 4 (DEGREES)	19.443
TORSION ANGLES. PERIOD 3 (DEGREES)	16.73
TORSION ANGLES. PERIOD 1 (DEGREES)	8.046
r_angle_refined_deg	2.074
r_angle_other_deg	1.398
r_chiral_restr	0.207
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2012
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	116

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 R01GM157729.