2VDD

Crystal Structure of the Open State of TolC Outer Membrane Component of Mutlidrug Efflux Pumps

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1EK9	PDB ENTRY 1EK9 CHAIN A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN WAS CRYSTALLISED FROM 0.1M HEPES 7.5, 5% ISOPROPANOL, 10% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.485	α = 90
b = 70.966	β = 100.61
c = 219.951	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	MARRESEARCH	SLITS	2007-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	3.3	29.8	98	0.15	7.46	3.3		26721		2.4

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	3.3	3.36	99.1		0.4	2.45	3.3

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 1EK9 CHAIN A	3.3	29.8	26721	1425	97.2	0.239	0.236	0.23	0.295	0.29	RANDOM	48.27

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]
0.09		-0.04	-0.02		-0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.602
r_dihedral_angle_3_deg	16.917
r_dihedral_angle_4_deg	15.624
r_dihedral_angle_1_deg	5.095
r_scangle_it	1.026
r_angle_refined_deg	0.979
r_mcangle_it	0.727
r_scbond_it	0.567
r_mcbond_it	0.397
r_nbtor_refined	0.289
r_symmetry_vdw_refined	0.195
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.114
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
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	9908
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing