9P0C | pdb_00009p0c

Crystal structure of Ca2+-bound RTX domain block V of adenylate cyclase toxin from Bordetella pertussis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CXL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289.15	Buffer: 40 mM polyamines, 100 mM glycylglycine and 2-Amino-2-methyl-1,3-propanediol (AMPD), pH 8.5. Precipitant: 31% v/v of 10% w/v PEG 20k, 50% w/v trimethylpropane (TMP), 2% w/v NDSB-195.

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.722	α = 90
b = 66.759	β = 93.226
c = 59.072	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 16M		2023-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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	1.7	37.7	98.4	0.097	7.2	3.8		31714

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.73	98.2		0.991	1.5

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	1.7	30.664	31628	1581	98.047	0.172	0.1705	0.1709	0.2082	0.2085	24.974

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]
-1.744		-1.247	0.102		1.771

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.369
r_dihedral_angle_3_deg	14.047
r_dihedral_angle_1_deg	7.548
r_dihedral_angle_2_deg	7.263
r_lrange_it	7.122
r_scangle_it	5.69
r_scbond_it	3.687
r_mcangle_it	3.048
r_mcbond_it	2.093
r_angle_refined_deg	1.486
r_nbtor_refined	0.306
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.161
r_xyhbond_nbd_refined	0.135
r_symmetry_metal_ion_refined	0.127
r_chiral_restr	0.108
r_metal_ion_refined	0.099
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2543
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	33

Software

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