10QF | pdb_000010qf

Crystal Structure of Treponema denticola Sialidase (TDE_0471)

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	7.4	296	25 mM Citric acid, 75 mM Bis-tris propane, pH 7.4, 20 mM Cadmium chloride, 25% PEG400, seeded

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.794	α = 90
b = 65.479	β = 106.783
c = 92.042	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	1.627	45.71	95.8	0.109	0.985	5.7	2.7		88676			12.73

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	1.63	1.67	88.5		1.033	0.571	1	2.7

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.627	45.709	88640	4601	95.527	0.165	0.1638	0.1711	0.1869	0.1954	17.401

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]
-1.579		-0.224	1.476		0.202

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.711
r_dihedral_angle_3_deg	12.444
r_dihedral_angle_2_deg	7.924
r_dihedral_angle_1_deg	7.366
r_lrange_it	5.906
r_lrange_other	5.741
r_scangle_it	3.168
r_scangle_other	3.167
r_scbond_it	2.601
r_scbond_other	2.6
r_angle_refined_deg	1.601
r_mcangle_other	1.422
r_mcangle_it	1.416
r_mcbond_it	0.915
r_mcbond_other	0.915
r_angle_other_deg	0.561
r_metal_ion_refined	0.308
r_symmetry_nbd_refined	0.241
r_nbd_refined	0.198
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.162
r_nbd_other	0.151
r_symmetry_xyhbond_nbd_refined	0.151
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.08
r_chiral_restr_other	0.018
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3910
Nucleic Acid Atoms
Solvent Atoms	479
Heterogen Atoms	114

Software

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