7WJF

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WJA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	14% PEG 3350, 400 mM ammonium citrate buffer (pH 7.0), 10 mM kojibiose

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.718	α = 90
b = 151.718	β = 90
c = 177.681	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	CCD	ADSC QUANTUM 270		2021-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

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	0.09	1	25	19.7		111324

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		1.235	0.848	2.8	18.9

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	44.46	111247	5468	99.96	0.171	0.1698	0.1907	30.748

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]
0.301	0.15		0.301		-0.976

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.593
r_dihedral_angle_3_deg	12.81
r_dihedral_angle_4_deg	12.488
r_dihedral_angle_1_deg	7.311
r_lrange_it	5.899
r_lrange_other	5.854
r_scangle_it	5.032
r_scangle_other	5.031
r_scbond_it	3.34
r_scbond_other	3.34
r_mcangle_other	3.086
r_mcangle_it	3.085
r_mcbond_it	2.406
r_mcbond_other	2.4
r_angle_refined_deg	1.563
r_angle_other_deg	1.42
r_nbd_refined	0.202
r_nbd_other	0.2
r_symmetry_nbd_refined	0.181
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.173
r_symmetry_xyhbond_nbd_refined	0.166
r_xyhbond_nbd_refined	0.13
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.077
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
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	580
Heterogen Atoms	55

Software

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