3IAX | pdb_00003iax

The crystal structure of the TolB box of Colicin A in complex with TolB reveals important differences in the recruitment of the common TolB translocation portal used by group A colicins

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C5K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	20% PEG 10000, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.691347	27.276892

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.955	α = 90
b = 40.174	β = 97.18
c = 80.868	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	IMAGE PLATE	RIGAKU RAXIS IV++	Mirror	2007-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	2.6	30	97.9	0.095	0.111	7.7	3.6		12220			16.6

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	2.6	2.67	96.6		0.347	0.405	3.7	3.7	1753

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	1C5K	2.6	30	12220	11636	583	97.97	0.193	0.19316	0.19005	0.2	0.25685	0.27	RANDOM	16.571

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]
0.31		0.1	1.35		-1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.836
r_dihedral_angle_4_deg	23.246
r_dihedral_angle_3_deg	20.753
r_dihedral_angle_1_deg	14.446
r_scangle_it	2.056
r_angle_refined_deg	1.774
r_scbond_it	1.315
r_mcangle_it	0.871
r_mcbond_it	0.468
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.231
r_symmetry_hbond_refined	0.231
r_chiral_restr	0.193
r_xyhbond_nbd_refined	0.175
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3089
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	8

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling