7WJD

Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase mutant D394A in complex with nigerotriose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	13% PEG 3350, 400 mM ammonium citrate buffer (pH 7.0), 10 mM nigerotriose

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.97	α = 90
b = 151.97	β = 90
c = 177.671	γ = 120

Symmetry
Space Group	P 63 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 PILATUS3 S 2M		2021-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

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	1.8	50	100	0.072	1	30.5	19.6		111675

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	1.8	1.9	100		1.505	0.841	2.6	20.2

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	7WJA	1.8	47.948	111610	5487	99.973	0.177	0.1757	0.1944	35.264

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]
0.483	0.242		0.483		-1.568

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.56
r_dihedral_angle_3_deg	13.005
r_dihedral_angle_4_deg	12.221
r_dihedral_angle_1_deg	7.403
r_lrange_it	5.96
r_lrange_other	5.941
r_scangle_it	5.31
r_scangle_other	5.309
r_scbond_it	3.658
r_scbond_other	3.658
r_mcangle_other	3.316
r_mcangle_it	3.315
r_mcbond_it	2.726
r_mcbond_other	2.721
r_angle_refined_deg	1.595
r_angle_other_deg	1.421
r_nbd_refined	0.204
r_nbd_other	0.182
r_nbtor_refined	0.178
r_symmetry_nbd_refined	0.174
r_symmetry_nbd_other	0.173
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_refined	0.069
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5988
Nucleic Acid Atoms
Solvent Atoms	480
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing
Coot	model building