8IUC

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae in complex with isomaltose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	300mM ammonium citrate, pH 7.0-8.0, 10mM TCEP, 12% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.938	α = 90
b = 194.09	β = 116.348
c = 111.88	γ = 90

Symmetry
Space Group	C 1 2 1

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 PILATUS 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)	Rrim I (All)	Rpim I (All)	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	1.56	48.54	98.2	0.072	0.088	0.049	0.999	13.2	6.1		326516

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.56	1.59			0.947	1.15	0.644	0.813	2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.56	44.71	326232	16344	98.263	0.188	0.1873	0.2114	26.71

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]
-2.046		1.149	-3.159		2.728

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.991
r_dihedral_angle_3_deg	14.994
r_dihedral_angle_2_deg	8.312
r_dihedral_angle_1_deg	7.063
r_lrange_it	5.342
r_lrange_other	5.315
r_scangle_it	3.648
r_scangle_other	3.648
r_scbond_it	2.501
r_scbond_other	2.5
r_angle_refined_deg	1.974
r_mcangle_other	1.942
r_mcangle_it	1.941
r_mcbond_it	1.454
r_mcbond_other	1.454
r_angle_other_deg	0.673
r_nbd_refined	0.229
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.188
r_symmetry_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.161
r_nbd_other	0.155
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.107
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15741
Nucleic Acid Atoms
Solvent Atoms	1414
Heterogen Atoms	189

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing