8QJK | pdb_00008qjk

Structure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	293	0.2MLiS04, 0.1M NaAcetate, 42.5% peg400

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.425	α = 90
b = 66.425	β = 90
c = 42.479	γ = 90

Symmetry
Space Group	I 4

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 X 16M		2022-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.76	46.97	89.1	1	14.3	13.3		5251

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.91			0.721

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	1.761	46.97	5251	218	56.615	0.245	0.2433	0.25	0.2724	0.27	41.01

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]
0.049			0.049		-0.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	14.408
r_dihedral_angle_3_deg	13.582
r_dihedral_angle_6_deg	13.063
r_dihedral_angle_1_deg	6.951
r_lrange_it	6.512
r_lrange_other	6.494
r_mcangle_it	4.312
r_mcangle_other	4.307
r_scangle_it	3.29
r_scangle_other	3.287
r_mcbond_it	2.55
r_mcbond_other	2.546
r_scbond_it	1.934
r_scbond_other	1.932
r_angle_refined_deg	1.112
r_angle_other_deg	0.947
r_symmetry_nbd_other	0.197
r_nbd_refined	0.194
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.146
r_nbd_other	0.139
r_symmetry_nbd_refined	0.111
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.049
r_bond_other_d	0.042
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	619
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	95

Software

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