6ZZ5

Structure of soluble SmhB of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		280.15	0.17 M ammonium sulphate, 25.5 % PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.94	α = 90
b = 113.95	β = 90
c = 130.37	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	80	PIXEL	DECTRIS PILATUS 6M-F		2018-09-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9159	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.84	65.185	99.8	0.139	0.078	1	9.5	6.7		66582

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.87			1.214	0.842	0.5	1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6GRK	1.84	65.185	66506	3268	99.661	0.189	0.1872	0.224	24.839

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]
-0.509			-1.266		1.775

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.939
r_dihedral_angle_4_deg	17.156
r_dihedral_angle_3_deg	13.555
r_lrange_it	8.513
r_lrange_other	8.512
r_scangle_it	8.001
r_scangle_other	8
r_scbond_it	6.34
r_scbond_other	6.34
r_dihedral_angle_1_deg	4.972
r_mcangle_other	3.596
r_mcangle_it	3.592
r_mcbond_it	3.13
r_mcbond_other	3.115
r_angle_refined_deg	1.759
r_angle_other_deg	1.542
r_symmetry_nbd_refined	0.391
r_symmetry_xyhbond_nbd_refined	0.329
r_nbd_refined	0.217
r_nbd_other	0.192
r_symmetry_nbd_other	0.173
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.161
r_ncsr_local_group_1	0.142
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5389
Nucleic Acid Atoms
Solvent Atoms	257
Heterogen Atoms	68

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing