1GIQ

Crystal Structure of the Enzymatic Componet of Iota-Toxin from Clostridium Perfringens with NADH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GIR	1GIR:THE ENZYMATIC COMPONENT IOTA-TOXIN WITH NADPH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1			277	PEG4000, NADH, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.2	α = 99.2
b = 54.44	β = 93.1
c = 103.38	γ = 106.9

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	283	CCD	ADSC QUANTUM			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-18B		Photon Factory	BL-18B

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	1.8	15	95.9	0.06	6	1.97	87691	87691			20.3

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	1.8	1.9	93.4		0.256

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1GIR:THE ENZYMATIC COMPONENT IOTA-TOXIN WITH NADPH	1.8	14.97	1	83233	8178	91	0.224	0.25	RANDOM	30.6

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]
0.2	0.38	-0.11	2.08	2.12	-2.28

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22.7
c_scangle_it	3.62
c_mcangle_it	2.54
c_scbond_it	2.4
c_mcbond_it	1.58
c_angle_deg	1.2
c_improper_angle_d	0.81
c_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6694
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	88

Software

Software
Software Name	Purpose
MOSFLM	data reduction
CNS	refinement
DPS	data reduction
CNS	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.