10QG | pdb_000010qg

Crystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	Q73QH2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	296	100 mM HEPES, pH 7.8, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 25 mM DANA for 20 min

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.811	α = 90
b = 65.547	β = 106.148
c = 91.679	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		2022-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0331	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.549	59.314	97.1	0.077	0.994	11.8	4.7		104014			9.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.59	94.6		0.274	0.943	4.5	4.7

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 (All)	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	1.549	59.314	104006	5239	96.852	0.139	0.1378	0.1505	0.153	0.1636	Random	14.886

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]
-1.307		-0.15	0.854		0.463

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	18.096
r_dihedral_angle_3_deg	12.54
r_dihedral_angle_2_deg	7.71
r_dihedral_angle_1_deg	7.588
r_lrange_it	4.657
r_lrange_other	4.424
r_scangle_it	2.526
r_scangle_other	2.526
r_scbond_it	2.094
r_scbond_other	2.093
r_dihedral_angle_other_3_deg	2.029
r_angle_refined_deg	1.656
r_mcangle_it	1.383
r_mcangle_other	1.383
r_mcbond_it	0.933
r_mcbond_other	0.923
r_angle_other_deg	0.579
r_symmetry_nbd_refined	0.364
r_nbd_other	0.274
r_nbd_refined	0.205
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.18
r_metal_ion_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.151
r_xyhbond_nbd_refined	0.131
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.086
r_symmetry_metal_ion_refined	0.069
r_bond_refined_d	0.013
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3918
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	97

Software

Software
Software Name	Purpose
REFMAC	refinement
Coot	model building
BUCCANEER	model building
PHASER	phasing
Aimless	data scaling
xia2	data reduction
DIALS	data reduction