6HSV | pdb_00006hsv

Engineered higher-order assembly of Cholera Toxin B subunits via the addition of C-terminal parallel coiled-coiled domains

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CHB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	Hampton Crystal Screen 2 condition #43: 0.2 M Ammonium Phosphate monobasic, 0.1 M Tris (pH 8.5), 50% v/v (+/-)-2-Methyl-2,4-pentanediol.

Crystal Properties
Matthews coefficient	Solvent content
3.54	65.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 179.16	α = 90
b = 179.16	β = 90
c = 192.02	γ = 120

Symmetry
Space Group	P 63

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 PILATUS 6M		2014-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96862	Diamond	I24

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	2.45	37.28	100	0.092	0.097	0.03	0.999	19	10.2		127892

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	2.45	2.51	100		0.698	0.744	0.346	0.864	3.2	8.4

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	3CHB	2.45	37.28	121547	6304	99.96	0.19639	0.19548	0.2	0.21378	0.21	RANDOM	55.917

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]
0.97	0.48		0.97		-3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.244
r_dihedral_angle_4_deg	26.331
r_dihedral_angle_3_deg	16.289
r_dihedral_angle_1_deg	15.048
r_long_range_B_refined	6.508
r_long_range_B_other	6.508
r_scangle_other	3.221
r_mcangle_it	2.423
r_mcangle_other	2.423
r_scbond_it	2.157
r_scbond_other	2.157
r_angle_refined_deg	1.794
r_mcbond_it	1.442
r_mcbond_other	1.441
r_angle_other_deg	1.367
r_chiral_restr	0.083
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	17187
Nucleic Acid Atoms
Solvent Atoms	584
Heterogen Atoms	247

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
Aimless	data scaling
MOLREP	phasing