7A27 | pdb_00007a27

Structure of soluble SmhA crystal form 2 of the tripartite alpha-pore forming toxin, Smh, from Serratia marcescens.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7A26

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		280	0.2M potassium nitrate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.24	α = 90
b = 92.58	β = 90
c = 221.1	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 EIGER2 XE 16M		2019-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9159	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.57	110.55	99.9	0.19	0.055	1	8.5	13		53914

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	2.57	2.61			2.129	0.595	0.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7A26	2.57	110.55	53847	2611	99.75	0.236	0.2357	0.23	0.247	0.25	72.64

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]
-1.09			10.982		-9.892

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.996
r_dihedral_angle_3_deg	14.581
r_dihedral_angle_4_deg	13.544
r_lrange_it	3.584
r_lrange_other	3.567
r_dihedral_angle_1_deg	3.253
r_mcangle_it	2.287
r_mcangle_other	2.287
r_scangle_it	2.1
r_scangle_other	2.1
r_angle_refined_deg	1.555
r_mcbond_it	1.345
r_mcbond_other	1.345
r_angle_other_deg	1.295
r_scbond_it	1.214
r_scbond_other	1.213
r_symmetry_nbd_refined	0.212
r_nbd_refined	0.204
r_nbd_other	0.195
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.149
r_xyhbond_nbd_refined	0.146
r_symmetry_xyhbond_nbd_refined	0.094
r_ncsr_local_group_1	0.094
r_ncsr_local_group_4	0.093
r_ncsr_local_group_3	0.091
r_ncsr_local_group_6	0.089
r_ncsr_local_group_5	0.087
r_ncsr_local_group_2	0.085
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10372
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms

Software

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