7WJE

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

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 nigerotetraose

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.751	α = 90
b = 151.751	β = 90
c = 177.656	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	0.095	1	22.2	19.7		111334

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		1.068	0.882	3.3	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	47.883	111269	5471	99.953	0.167	0.1654	0.1888	30.183

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]
0.333	0.166		0.333		-1.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.746
r_dihedral_angle_3_deg	12.594
r_dihedral_angle_4_deg	12.404
r_dihedral_angle_1_deg	7.361
r_lrange_it	5.806
r_lrange_other	5.806
r_scangle_it	4.905
r_scangle_other	4.905
r_scbond_it	3.245
r_scbond_other	3.245
r_mcangle_other	2.895
r_mcangle_it	2.894
r_mcbond_it	2.247
r_mcbond_other	2.24
r_angle_refined_deg	1.57
r_angle_other_deg	1.416
r_nbd_refined	0.202
r_nbd_other	0.183
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.152
r_xyhbond_nbd_refined	0.145
r_symmetry_xyhbond_nbd_refined	0.113
r_chiral_restr	0.081
r_symmetry_nbtor_other	0.079
r_symmetry_xyhbond_nbd_other	0.039
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	638
Heterogen Atoms	65

Software

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