10QH | pdb_000010qh

Crystal Structure of Treponema denticola Sialidase (TDE_0471) Bound to Neu5Ac (NANA)

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	8.2	296	100 mM Tris, pH 8.2, 20 mM Cadmium chloride, 25% PEG400, soak in mother liquor with 15 mM Neu5Ac

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.734	α = 90
b = 65.371	β = 106.19
c = 92.021	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	1.56	57.95	97.3	0.075	0.997	11.2	4.6		102901			12.28

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	1.56	1.6	90.2		0.422	0.912	3	4.4

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	1.56	57.95	97730	5155	97.25	0.14267	0.14184	0.1429	0.15848	0.1594	RANDOM	21.4

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]
-1.6		-0.24	0.46		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.78
r_dihedral_angle_2_deg	8.759
r_dihedral_angle_1_deg	7.607
r_long_range_B_refined	5.466
r_long_range_B_other	5.257
r_scangle_other	3.115
r_scbond_it	3.095
r_scbond_other	3.095
r_angle_refined_deg	1.689
r_mcangle_other	1.689
r_mcangle_it	1.688
r_mcbond_it	1.127
r_mcbond_other	1.127
r_angle_other_deg	0.578
r_chiral_restr	0.086
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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	3915
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	91

Software

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