9P0D | pdb_00009p0d

Crystal structure of Sr2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	Buffer: 100 mM amino acids, 100 mM imidazole, 100 mM 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.5. Precipitant: 37.5% v/v of 25% v/v 2-Methyl-2,4-pentanediol (MPD), 25% w/v PEG 1000, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.54	α = 90
b = 73.095	β = 90
c = 73.839	γ = 90

Symmetry
Space Group	I 2 2 2

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		2024-05-16	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.76910	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.5	30.95	98.6	0.303	5	13.2		26872			15.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	94.2		1.86	2.03	1.2

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	MAD	FREE R-VALUE	1.502	30.949	26846	1314	98.089	0.176	0.1745	0.1877	0.2014	0.2115	21.48

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]
-1.424			-0.758		2.182

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.595
r_dihedral_angle_3_deg	13.754
r_dihedral_angle_2_deg	8.612
r_lrange_it	7.728
r_dihedral_angle_1_deg	6.86
r_scangle_it	5.852
r_scbond_it	4.038
r_mcangle_it	3.053
r_mcbond_it	2.048
r_angle_refined_deg	1.768
r_symmetry_nbd_refined	0.357
r_nbtor_refined	0.315
r_nbd_refined	0.265
r_metal_ion_refined	0.224
r_symmetry_xyhbond_nbd_refined	0.201
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.128
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1145
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
SCALA	data scaling
CRANK2	phasing