Experiment: 9BA7

Crystal structure of Vibrio cholerae N150T NFeoB variant with a single GDP molecule bound

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8VWL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	24% (w/v) PEG 3350, 0.1 M bis-Tris (pH 5.5), 30 mM magnesium chloride, 0.2 M ammonium sulfate, 25 mM Tris (pH 8), 5% (w/v) glycerol, 100 mM NaCl, 1 mM TCEP*HCl, 3 mM GDP

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 202.466	α = 90
b = 50.093	β = 90
c = 62.249	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 16M		2024-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-2	0.97934	NSLS-II	17-ID-2

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	2.88	33.94	99.4	0.997	8.8	5.3		14956			79.56

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	2.88	2.93			0.33

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	2.88	33.94	1.34	14940	710	99.32	0.2167	0.2139	0.2134	0.2682	0.2665	85.16

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	17.4035
f_angle_d	1.1546
f_chiral_restr	0.0607
f_bond_d	0.0087
f_plane_restr	0.0078

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3913
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	35

Software

Software
Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing