10JY | pdb_000010jy

Crystal structure of heme binding PAS domain from one component transcription factor, FG214 reduced with dithionite

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		D_1000301930 to be deposited

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2M Sodium formate, 0.2M Ammonium acetate, 0.2M Sodium citrate tribasic dihydrate, 0.2M Potassium sodium tartrate tetrahydrate, 0.2M Sodium oxamate, 0.2M 1,6-Hexanediol, 0.2M 1-Butanol 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol, 0.4M Imidazole, 0.6M MES monohydrate, 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.03	α = 90
b = 65.21	β = 90
c = 105.87	γ = 90

Symmetry
Space Group	P 21 21 21

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 9M		2025-03-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9786	NSLS-II	19-ID

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	1.648	55.523	100	0.999	11	7.4		393593			31.32

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	1.648	1.677			0.382

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	45.32	1.35	53262	2635	99.77	0.1889	0.1876	0.1904	0.2154	0.2182	38.67

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.0081
f_angle_d	1.1172
f_chiral_restr	0.057
f_plane_restr	0.0169
f_bond_d	0.0106

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2246
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	105

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
autoPROC	data processing