3ZJX

Clostridium perfringens epsilon toxin mutant H149A bound to octyl glucoside

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UYJ	PDB ENTRY 1UYJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.85 M AMMONIUM DIHYDROGEN PHOSPHATE AND 0.5% (W/V) OCTYLGLUCOSIDE

Crystal Properties
Matthews coefficient	Solvent content
4.39	72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.709	α = 90
b = 123.709	β = 90
c = 127.314	γ = 120

Symmetry
Space Group	P 3

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	RIGAKU SATURN 944		2012-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE

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	2.4	21.56	100	0.06	12.3	3.7		85072		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	2.4	2.49	99.9		0.44	1.2	2.2

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	PDB ENTRY 1UYJ	2.4	21.56	80521	4258	99.48	0.24817	0.2467	0.22	0.27543	0.24	RANDOM	52.565

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]
11.39			11.39		-22.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.3
r_dihedral_angle_4_deg	22.391
r_dihedral_angle_3_deg	15.696
r_long_range_B_refined	7.263
r_long_range_B_other	7.262
r_dihedral_angle_1_deg	6.233
r_scangle_other	4.817
r_mcangle_it	4.358
r_mcangle_other	4.358
r_scbond_it	3.139
r_scbond_other	3.135
r_mcbond_it	2.862
r_mcbond_other	2.862
r_angle_refined_deg	1.384
r_angle_other_deg	0.908
r_chiral_restr	0.08
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8443
Nucleic Acid Atoms
Solvent Atoms	459
Heterogen Atoms	100

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
PHASER	phasing