8TDH | pdb_00008tdh

Structure of trehalose bound Alistipes sp. Glucoside-3-dehydrogenase AL3

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.25 M Sodium Malonate 17% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 186.581	α = 90
b = 57.221	β = 106.584
c = 224.962	γ = 90

Symmetry
Space Group	I 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 9M		2023-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0332	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.95	162.27	89.9	0.141	0.199	0.141	0.95	3.5	2.7		43707

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.95	3.06			0.462	0.654	0.462	0.497		1.9

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.95	162.267	43706	2195	89.655	0.198	0.1949	0.2056	0.2471	0.2471	RANDOM	40.815

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]
-3.91		1.823	-1.193		3.412

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.604
r_dihedral_angle_6_deg	14.774
r_dihedral_angle_2_deg	10.348
r_dihedral_angle_1_deg	7.848
r_angle_refined_deg	5.641
r_lrange_it	3.573
r_lrange_other	3.562
r_scangle_it	2.453
r_scangle_other	2.453
r_scbond_it	1.428
r_scbond_other	1.428
r_dihedral_angle_other_2_deg	0.947
r_mcangle_it	0.789
r_mcangle_other	0.789
r_angle_other_deg	0.682
r_mcbond_it	0.436
r_mcbond_other	0.436
r_nbd_other	0.228
r_nbd_refined	0.223
r_symmetry_nbd_other	0.213
r_symmetry_xyhbond_nbd_refined	0.208
r_nbtor_refined	0.195
r_xyhbond_nbd_refined	0.194
r_symmetry_nbd_refined	0.188
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.09
r_ncsr_local_group_3	0.075
r_ncsr_local_group_4	0.075
r_ncsr_local_group_5	0.075
r_ncsr_local_group_1	0.074
r_ncsr_local_group_2	0.073
r_ncsr_local_group_6	0.071
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14208
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	682

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing