7WJC

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

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	13% PEG 3350, 400 mM ammonium citrate buffer (pH 7.0), 10 mM nigerose

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.37	α = 90
b = 151.37	β = 90
c = 177.235	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	1.75	50	100	0.067	1	30.4	19.8		120135

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	1.75	1.84	100		1.191	0.869	2.9	20

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	1.75	47.763	120083	6004	99.984	0.167	0.1657	0.1904	32.269

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]
0.525	0.262		0.525		-1.702

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.028
r_dihedral_angle_4_deg	12.608
r_dihedral_angle_3_deg	12.505
r_dihedral_angle_1_deg	7.299
r_lrange_it	5.889
r_lrange_other	5.843
r_scangle_it	5.182
r_scangle_other	5.181
r_scbond_it	3.533
r_scbond_other	3.533
r_mcangle_other	3.036
r_mcangle_it	3.035
r_mcbond_it	2.473
r_mcbond_other	2.468
r_angle_refined_deg	1.613
r_angle_other_deg	1.444
r_nbd_refined	0.204
r_nbd_other	0.191
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.176
r_symmetry_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.155
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.011
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	552
Heterogen Atoms	63

Software

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