7ZHM | pdb_00007zhm

Salmonella enterica Rhs1 C-terminal toxin TreTu complex with TriTu immunity protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		unpublished

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.001M ZnSulfate heptahydrate; 0.05M HEPES 7.8; 28% PEG600

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.645	α = 90
b = 94.036	β = 110.069
c = 61.305	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	100	PIXEL	DECTRIS EIGER X 9M		2021-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	1.281493	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.7	49.11	99.8	0.247	0.271	0.11	0.974	5.9	5.9		17246

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	100		0.768	0.848	0.354	0.675		5.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	unpublished	2.7	49.11	16319	894	99.67	0.21596	0.21376	0.22	0.25696	0.26	RANDOM	41.168

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]
-1.75		1.17	2.11		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.665
r_dihedral_angle_4_deg	18.26
r_dihedral_angle_3_deg	13.366
r_long_range_B_refined	10.99
r_long_range_B_other	10.979
r_scangle_other	10.053
r_scbond_it	7.977
r_scbond_other	7.975
r_dihedral_angle_1_deg	5.712
r_mcangle_other	5.702
r_mcangle_it	5.696
r_mcbond_it	4.1
r_mcbond_other	4.081
r_angle_refined_deg	1.002
r_angle_other_deg	0.899
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3184
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	92

Software

Software
Software Name	Purpose
PDB-REDO	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing