7WJA | pdb_00007wja

Crystal structure of Lactococcus lactis subsp. cremoris GH31 alpha-1,3-glucosidase, P6322 space group

X-RAY DIFFRACTION

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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)

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.56	α = 90
b = 151.56	β = 90
c = 176.611	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	1.85	50	100	0.091	1	24.7	19.7		101843

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	1.85	1.95	100		1.144	0.882	3	18.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	FREE R-VALUE	1.85	49.659	101725	5055	99.917	0.166	0.1653	0.18	0.1876	0.2	32.36

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]
0.206	0.103		0.206		-0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.167
r_dihedral_angle_4_deg	14.825
r_dihedral_angle_3_deg	13.241
r_dihedral_angle_1_deg	7.389
r_lrange_it	6.745
r_lrange_other	6.727
r_scangle_it	6.125
r_scangle_other	6.125
r_scbond_it	4.262
r_scbond_other	4.262
r_mcangle_other	3.651
r_mcangle_it	3.65
r_mcbond_it	2.993
r_mcbond_other	2.986
r_angle_refined_deg	1.769
r_angle_other_deg	1.487
r_nbd_other	0.238
r_symmetry_nbd_refined	0.237
r_nbd_refined	0.207
r_nbtor_refined	0.181
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.092
r_symmetry_xyhbond_nbd_other	0.083
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.013
r_gen_planes_refined	0.012
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	577
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
CRANK2	phasing
Coot	model building