7WJB | pdb_00007wjb

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

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)

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.362	α = 90
b = 151.362	β = 90
c = 177.263	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		2021-03-07	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	2	50	100	0.091	1	42	39.6		81029

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	100		0.947	4.7	40.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7WJA	2	46.617	80852	4083	99.814	0.181	0.18	0.19	0.2081	0.21	38.286

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]
0.855	0.427		0.855		-2.773

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.806
r_dihedral_angle_3_deg	13.637
r_dihedral_angle_4_deg	12.411
r_dihedral_angle_1_deg	7.488
r_lrange_it	6.821
r_lrange_other	6.818
r_scangle_it	6.054
r_scangle_other	6.053
r_scbond_it	4.283
r_scbond_other	4.282
r_mcangle_it	4.086
r_mcangle_other	4.086
r_mcbond_it	3.393
r_mcbond_other	3.391
r_angle_refined_deg	1.695
r_angle_other_deg	1.417
r_symmetry_nbd_refined	0.212
r_nbd_refined	0.201
r_nbd_other	0.181
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.176
r_symmetry_xyhbond_nbd_other	0.144
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.12
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5991
Nucleic Acid Atoms
Solvent Atoms	351
Heterogen Atoms	56

Software

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