7P4D

Crystal Structure of Agd31B, alpha-transglucosylase in Glycoside Hydrolase Family 31, in complex with covalent Cyclophellitol Sulfamidate probe KK130

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4B9Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	1.8 M AMMONIUM SULFATE, 0.1 M HEPES (PH 7.0), 2% PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 197.076	α = 90
b = 197.076	β = 90
c = 102.149	γ = 120

Symmetry
Space Group	P 6 2 2

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-F		2019-07-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97950	Diamond	I04

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	1.85	98.54	100	0.133	0.136	0.027	0.999	14.2	24.7		99190

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	1.85	1.88			2.685	2.741	0.545	0.696	1.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4b9y	1.85	98.538	99175	4583	99.947	0.19	0.1884	0.2216	39.213

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]
-1.224	-0.612		-1.224		3.972

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.51
r_dihedral_angle_4_deg	16.169
r_dihedral_angle_3_deg	14.676
r_lrange_it	7.942
r_lrange_other	7.914
r_dihedral_angle_1_deg	7.687
r_scangle_it	6.377
r_scangle_other	6.263
r_mcangle_it	4.544
r_mcangle_other	4.544
r_scbond_it	4.244
r_scbond_other	4.158
r_mcbond_it	3.438
r_mcbond_other	3.437
r_angle_other_deg	2.326
r_angle_refined_deg	1.62
r_chiral_restr_other	0.963
r_symmetry_nbd_other	0.217
r_nbd_other	0.211
r_nbd_refined	0.199
r_symmetry_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.157
r_symmetry_nbd_refined	0.146
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.078
r_bond_other_d	0.035
r_symmetry_xyhbond_nbd_other	0.032
r_gen_planes_other	0.014
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6237
Nucleic Acid Atoms
Solvent Atoms	485
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
REFMAC	phasing