9P6C | pdb_00009p6c

RTX domain block V of adenylate cyclase toxin with mutations D1533N, A1542N, D1560N, S1569N, D1587N, H1598N, H1608N

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	6.5	289	Buffer: 0.1 M MES, 0.1 M imidazole, pH 6.5 Precipitant: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD; 0.02 M of each amino acid (L-glutamate, DL-alanine, glycine, DL-lysine, and DL-serine) Protein solution: 50 mM Tris, 150 mM NaCl, 10 mM CaCl2, pH 8

Crystal Properties
Matthews coefficient	Solvent content
2.05	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.305	α = 84.13
b = 38.003	β = 81.47
c = 57.016	γ = 67.61

Symmetry
Space Group	P 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 EIGER2 XE 16M		2024-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	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	1.99	30.58	85.4	0.103	6.6	3.8		14967			18.2

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	1.99	2.04	85.3		0.292

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 (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	FREE R-VALUE	1.99	30.58	14115	766	85.45	0.23164	0.22847	0.2285	0.29235	0.2928	RANDOM	38.338

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]
-1.82	1.07	-1.03	-0.42	1.34	2.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.155
r_dihedral_angle_1_deg	8.578
r_long_range_B_refined	7.52
r_dihedral_angle_2_deg	4.605
r_mcangle_it	4.026
r_scbond_it	3.427
r_mcbond_it	2.633
r_angle_refined_deg	1.317
r_chiral_restr	0.111
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2276
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing