2VSE | pdb_00002vse

Structure and mode of action of a mosquitocidal holotoxin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CB4	PDB ENTRY 2CB4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.3		0.1 M TRIS, PH 8.3 3% (W/V) PEG-6000 250 MM KCL 4% MPD

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.963	α = 90
b = 130.963	β = 90
c = 396.061	γ = 120

Symmetry
Space Group	H 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	MARREASEARCH		2006-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2		BESSY	14.2

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	2.5	75	99.9	0.09	0.084	18.6	7.1		87586		2

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	2.5	2.58	99.8		0.38	0.48	3.3	5

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 2CB4	2.5	74.54	83206	4379	100	0.194	0.192	0.19	0.234	0.23	RANDOM	49.23

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]
1.46	0.73		1.46		-2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.53
r_dihedral_angle_4_deg	18.378
r_dihedral_angle_3_deg	15.837
r_dihedral_angle_1_deg	6.63
r_scangle_it	1.646
r_angle_refined_deg	1.201
r_scbond_it	1.072
r_mcangle_it	0.556
r_nbtor_refined	0.309
r_mcbond_it	0.302
r_symmetry_vdw_refined	0.277
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13480
Nucleic Acid Atoms
Solvent Atoms	676
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing