3EB7 | pdb_00003eb7

Crystal Structure of Insecticidal Delta-Endotoxin Cry8Ea1 from Bacillus Thuringiensis at 2.2 Angstroms Resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 407.282	α = 90
b = 47.956	β = 91.12
c = 103.121	γ = 90

Symmetry
Space Group	C 1 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	CCD	ADSC QUANTUM 315	mirrors	2006-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	204.1	97.4	0.137	0.137	12.3	4.5	101555	98915	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.28	84.1		0.46	0.46	2.07	2.8	10105

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1CIY	2.3	43.2	1	1	80780	79964	8885	98.99	0.17103	0.16913	0.16235	0.16	0.23009	0.23	RANDOM	26.555

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]
-1.43		0.74	0.28		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.91
r_dihedral_angle_4_deg	19.997
r_dihedral_angle_3_deg	18.285
r_dihedral_angle_1_deg	6.716
r_scangle_it	3.659
r_scbond_it	2.399
r_angle_refined_deg	1.575
r_mcangle_it	1.454
r_mcbond_it	0.856
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.91
r_dihedral_angle_4_deg	19.997
r_dihedral_angle_3_deg	18.285
r_dihedral_angle_1_deg	6.716
r_scangle_it	3.659
r_scbond_it	2.399
r_angle_refined_deg	1.575
r_mcangle_it	1.454
r_mcbond_it	0.856
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.215
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.195
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14049
Nucleic Acid Atoms
Solvent Atoms	1101
Heterogen Atoms	77

Software

Software
Software Name	Purpose
ADSC	data collection
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
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.