6ZZH

Structure of soluble SmhB crystal form 2 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	0.22M Magnesium chloride hexahydrate 0.1M Na acetate pH 5.15, 26% (w/v) PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.931	α = 90
b = 49.729	β = 118.427
c = 99.495	γ = 90

Symmetry
Space Group	P 1 21 1

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		2020-02-23	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	1.86	87.51	90.2	0.1	0.044	0.8	10.4	10.4		50442

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	1.86	1.88			0.899	0.525	0.6

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	6ZZ5	1.86	87.498	50442	2521	72.222	0.215	0.2133	0.2471	29.312

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]
-0.76		0.738	0.026		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.989
r_dihedral_angle_4_deg	14.346
r_dihedral_angle_3_deg	13.231
r_lrange_it	6.225
r_lrange_other	6.217
r_scangle_it	4.568
r_scangle_other	4.568
r_dihedral_angle_1_deg	3.667
r_mcangle_it	2.967
r_mcangle_other	2.966
r_scbond_it	2.937
r_scbond_other	2.936
r_mcbond_it	1.931
r_mcbond_other	1.929
r_angle_refined_deg	1.656
r_angle_other_deg	1.513
r_symmetry_xyhbond_nbd_other	0.279
r_nbd_other	0.265
r_symmetry_nbd_refined	0.252
r_nbd_refined	0.226
r_symmetry_xyhbond_nbd_refined	0.196
r_xyhbond_nbd_refined	0.188
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.164
r_ncsr_local_group_1	0.122
r_chiral_restr	0.085
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5426
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms

Software

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