7FE3

Crystal structure of GH65 alpha-1,2-glucosidase from Flavobacterium johnsoniae

X-RAY DIFFRACTION

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Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 122.83	α = 90
b = 193.97	β = 116.601
c = 111.735	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 PILATUS3 S 2M		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)	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	1.54	50	99.7	0.05	0.054	0.021	1	19.9	6.8		342453

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	1.54	1.62			0.916	0.992	0.379	0.846	2.3

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	SAD	FREE R-VALUE	1.54	48.54	340941	16770	99.292	0.172	0.1709	0.1918	29.102

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]
-0.698		0.791	-1.879		1.188

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.817
r_dihedral_angle_3_deg	13.173
r_dihedral_angle_4_deg	13.15
r_dihedral_angle_1_deg	6.849
r_lrange_it	4.164
r_lrange_other	4.073
r_scangle_it	2.398
r_scangle_other	2.398
r_scbond_it	1.54
r_scbond_other	1.54
r_angle_refined_deg	1.501
r_mcangle_it	1.477
r_mcangle_other	1.477
r_angle_other_deg	1.416
r_mcbond_it	0.983
r_mcbond_other	0.983
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.208
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.171
r_nbd_other	0.149
r_symmetry_xyhbond_nbd_refined	0.133
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.08
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15741
Nucleic Acid Atoms
Solvent Atoms	1452
Heterogen Atoms	104

Software

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