9G7P | pdb_00009g7p

Crystal structure of Shewanella putrefaciens PE-like toxin, Spx

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294.15	0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 (condition C10 of the PACT premier Screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.196	α = 90
b = 121.196	β = 90
c = 125.216	γ = 120

Symmetry
Space Group	P 31

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 EIGER2 XE 16M		2021-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.79	104.83	100	0.28	0.287	0.062	0.997	7.5	21.5		193517

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	1.79	1.82	99.7		3.695	3.784	0.811	0.339	0.4	21.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.861	104.83	172116	8476	99.694	0.187	0.185	0.1837	0.2204	0.2202	34.028

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]
0.486	0.243		0.486		-1.576

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.939
r_dihedral_angle_4_deg	15.838
r_dihedral_angle_3_deg	11.536
r_dihedral_angle_1_deg	6.731
r_lrange_it	5.49
r_lrange_other	5.44
r_scangle_it	3.686
r_scangle_other	3.686
r_mcangle_it	2.876
r_mcangle_other	2.876
r_scbond_it	2.247
r_scbond_other	2.246
r_mcbond_it	1.79
r_mcbond_other	1.789
r_angle_refined_deg	1.283
r_angle_other_deg	1.221
r_metal_ion_refined	0.255
r_symmetry_nbd_refined	0.245
r_nbd_refined	0.19
r_symmetry_nbd_other	0.179
r_nbd_other	0.176
r_nbtor_refined	0.152
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_other	0.079
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.053
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13905
Nucleic Acid Atoms
Solvent Atoms	1241
Heterogen Atoms	40

Software

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