10QI | pdb_000010qi

Crystal Structure of Treponema denticola Sialidase (TDE_0471) D165A mutant bound to 3'-sialyllactose (only Neu5Ac visible)

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	6.5	296	100 mM Bis-tris, pH 6.5, 20 mM Cadmium chliride, 23% PEG400, 5 mM 3'-sialyllactose

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.445	α = 90
b = 66.077	β = 106.62
c = 93.115	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 PILATUS 6M		2023-03-18	M	SINGLE WAVELENGTH

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

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	1.81	46.172	99.7	0.174	0.979	4.8	2.9		69062			11.5

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	1.81	1.86	99.5		1.108	0.429	1.2	2.9

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	1.81	46.172	69036	3493	99.554	0.166	0.1649	0.1751	0.1898	0.1993	16.484

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]
-0.957		-0.464	1.227		0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.452
r_dihedral_angle_3_deg	12.968
r_dihedral_angle_2_deg	8.716
r_dihedral_angle_1_deg	7.841
r_lrange_it	5.461
r_lrange_other	5.196
r_scangle_it	2.836
r_scangle_other	2.835
r_scbond_it	2.153
r_scbond_other	2.152
r_angle_refined_deg	1.863
r_mcangle_it	1.597
r_mcangle_other	1.597
r_mcbond_it	1.005
r_mcbond_other	1.005
r_angle_other_deg	0.627
r_metal_ion_refined	0.502
r_symmetry_nbd_refined	0.248
r_nbd_refined	0.198
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.155
r_nbd_other	0.122
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.087
r_symmetry_metal_ion_refined	0.043
r_symmetry_xyhbond_nbd_other	0.036
r_bond_refined_d	0.014
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	3889
Nucleic Acid Atoms
Solvent Atoms	495
Heterogen Atoms	59

Software

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