3FU1 | pdb_00003fu1

Crystal structure of the major pseudopilin from the type 2 secretion system of Vibrio cholerae

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	22.5% PEG 3350, 0.1M NA ACETATE, 0.04M ZN ACETATE, pH 5.0, vapor diffusion, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.638	α = 90
b = 64.749	β = 90
c = 65.041	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 325 mm CCD		2007-11-15	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2007-11-15	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2
2	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.28344	SSRL	BL9-2

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
1,2	1.9	29	97.1	0.087	24.016	6.7		17045			24

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)
1,2	1.9	1.97	78.8		0.512	2.1	4.1	1373

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	27.28	16995	830	96.88	0.18	0.178	0.2	0.223	0.24	RANDOM	20.242

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]
-1.04			-0.5		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.366
r_dihedral_angle_3_deg	13.395
r_dihedral_angle_4_deg	10.411
r_dihedral_angle_1_deg	5.349
r_scangle_it	2.332
r_scbond_it	1.429
r_angle_refined_deg	1.187
r_mcangle_it	0.835
r_angle_other_deg	0.826
r_mcbond_it	0.444

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.366
r_dihedral_angle_3_deg	13.395
r_dihedral_angle_4_deg	10.411
r_dihedral_angle_1_deg	5.349
r_scangle_it	2.332
r_scbond_it	1.429
r_angle_refined_deg	1.187
r_mcangle_it	0.835
r_angle_other_deg	0.826
r_mcbond_it	0.444
r_mcbond_other	0.115
r_chiral_restr	0.065
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1755
Nucleic Acid Atoms
Solvent Atoms	224
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.