5VGC

Crystal structure of the NleG5-1 effector (C200A) from Escherichia coli O157:H7 str. Sakai

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	293	20% P3350, 0.2 M CaCl2, 2% Hexanediol, 20 mM Tris pH 9.0, 0.2 M NaCl, 0.3 M KCl2

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.376	α = 90
b = 151.376	β = 90
c = 87.983	γ = 120

Symmetry
Space Group	P 65 2 2

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	RAYONIX MX-300		2016-06-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	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	2.55	50.01	98.9	0.046	0.046	0.021	1	36.38	6.7		19632		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	100		0.638	0.494	1.2	6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2KKY	2.6	50.01	15593	1739	92.25	0.25015	0.24474	0.29704	RANDOM	83.011

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]
0.02	0.01		0.02		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.248
r_long_range_B_refined	29.174
r_long_range_B_other	29.171
r_mcangle_it	23.896
r_mcangle_other	23.89
r_scangle_other	18.386
r_dihedral_angle_4_deg	16.436
r_mcbond_other	15.883
r_mcbond_it	15.88
r_dihedral_angle_3_deg	15.745
r_scbond_it	12.19
r_scbond_other	12.148
r_dihedral_angle_1_deg	5.711
r_angle_refined_deg	1.344
r_angle_other_deg	0.965
r_chiral_restr	0.077
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3276
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing