9NJ0 | pdb_00009nj0

GlfT2 from Nocardia brasiliensis Bound to Galf Trisaccharide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	9DTP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293.15	6 mg/mL protein, 0.2% Triton X-100, 0.066 M imidazole, 2 mM magnesium chloride, 8.75% w/v PEG1000, 8.75% w/v PEG3350, 8.75% v/v MPD

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.784	α = 90
b = 204.965	β = 90
c = 294.126	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		2023-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.92	NSLS-II	17-ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	3.2	34.61	94.9	0.135	5.5	5.2		101657

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	3.2	3.31	94.73		0.435	0.89	1.6	5.27

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3.2	34.61	101657		92.08	0.2006	0.1997	0.2002	0.248	0.249	51.81

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	12.2398
f_angle_d	0.607
f_chiral_restr	0.0427
f_plane_restr	0.0046
f_bond_d	0.0028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	39120
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	459

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building