9DSF | pdb_00009dsf

Cyanide-ligated Bordetella pertussis globin coupled sensor regulatory domain S68A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M9A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	294.15	10 mM Tris, 0.2 M Calcium Acetate, 10% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2	38.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.958	α = 90
b = 49.702	β = 110.56
c = 67.994	γ = 90

Symmetry
Space Group	C 1 2 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	Horizontal pre-focus bimorph mirror & KB bimorph mirrors	2023-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.9793	NSLS-II	17-ID-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.85	46.67	99.48	0.026	0.992	21.1	3.4		38802			26.73

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.916	99.64		0.21	0.886	2	3.4

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	THROUGHOUT	1.85	46.67	36907	1896	99.45	0.20855	0.20704	0.2133	0.23862	0.2492	RANDOM	27.359

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]
-1.04		-0.92	1.13		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.28
r_dihedral_angle_4_deg	15.263
r_dihedral_angle_3_deg	13.87
r_dihedral_angle_1_deg	4.857
r_long_range_B_refined	2.74
r_long_range_B_other	2.711
r_scangle_other	1.448
r_mcangle_it	1.419
r_mcangle_other	1.418
r_angle_other_deg	1.169
r_angle_refined_deg	1.141
r_scbond_it	0.849
r_scbond_other	0.842
r_mcbond_it	0.813
r_mcbond_other	0.813
r_chiral_restr	0.049
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3647
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	141

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing