1YC9

The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	MPD, Tris, NaCl, beta-DDM, octyl-beta-glucoside, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Properties
Matthews coefficient	Solvent content
3.16	60.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.458	α = 90
b = 71.458	β = 90
c = 190.702	γ = 120

Symmetry
Space Group	P 3 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 4		2004-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9686	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	63.6	100			53358	53358

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8		100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	63.6	53358	53358	2708	99.96	0.19038	0.19038	0.1887	0.22119	RANDOM	23.748

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]
1.8	0.9		1.8		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	8.832
r_scangle_it	5.175
r_scbond_it	3.202
r_mcangle_it	1.939
r_angle_refined_deg	1.751
r_mcbond_it	1.089
r_angle_other_deg	1.055
r_symmetry_vdw_other	0.302
r_nbd_other	0.258
r_chiral_restr	0.254
r_xyhbond_nbd_refined	0.236
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.155
r_nbtor_other	0.091
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3125
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	22

Software

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