3CVZ | pdb_00003cvz

Structural insights into the molecular organization of the S-layer from Clostridium difficile

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	291	25% PEG 1500, 0.1M SPG buffer, pH 4.0, vapor diffusion, sitting drop, temperature 291K
2	VAPOR DIFFUSION, SITTING DROP	4.3	291	20% PEG 1500, 0.1M SPG buffer, pH 4.3, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.059	α = 90
b = 107.059	β = 90
c = 190.617	γ = 120

Symmetry
Space Group	P 64

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 225 mm CCD		2007-06-03	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2007-10-06	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	1.117	SRS	PX10.1
2	SYNCHROTRON	SRS BEAMLINE PX10.1	0.98006, 0.98035, 0.90651	SRS	PX10.1

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	2.13	100	99.8	0.087	9.4	17.8		68870

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.13	2.21	99.7			10.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	2.4	46.358	1.34	47747	1395	99	0.2328	0.2309	0.22	0.294	0.29	80.39

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]
11.323			11.323		-22.646

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.934
f_angle_d	1.23
f_chiral_restr	0.073
f_bond_d	0.01
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7250
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

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.