3EZJ

Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5	298	1.0M NA/K PHOSPHATE, pH 5.0, vapor diffusion, sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.52	α = 90
b = 98.52	β = 90
c = 402.1	γ = 120

Symmetry
Space Group	P 31 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	MARMOSAIC 325 mm CCD		2007-05-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2		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	2.4	50	91.7	0.086				86152		-3	57.73

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	2.8	2.9	91.7		0.767	2.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.8	47.67	55400	2813	97	0.194	0.192	0.239	RANDOM	50.77

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]
-0.12	-0.06		-0.12		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.344
r_dihedral_angle_4_deg	16.752
r_dihedral_angle_3_deg	14.37
r_dihedral_angle_1_deg	5.581
r_scangle_it	1.189
r_angle_refined_deg	1.063
r_angle_other_deg	0.795
r_scbond_it	0.752
r_mcangle_it	0.479
r_mcbond_it	0.43
r_symmetry_hbond_refined	0.21
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.203
r_symmetry_vdw_other	0.193
r_nbd_other	0.188
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.152
r_nbtor_other	0.081
r_chiral_restr	0.062
r_mcbond_other	0.053
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9740
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	44

Software

Software
Software Name	Purpose
XSCALE	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SHELXD	phasing