8IUB

Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae in complex with isomaltotriose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	100mM Tris-HCl, pH 8.5-9.0, 200mM lithium sulfate, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.911	α = 90
b = 91.058	β = 90
c = 137.354	γ = 90

Symmetry
Space Group	P 21 21 21

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		2022-05-15	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	1.18	45.78	99.9	0.063	0.069	0.019	1	19	12.5		173012

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	1.18	1.2			0.975	1.065	0.302	0.804	2.5

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	1.18	45.57	172910	8674	99.81	0.164	0.1626	0.1896	14.527

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]
-0.318			0.528		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.568
r_dihedral_angle_3_deg	13.328
r_dihedral_angle_2_deg	10.228
r_dihedral_angle_1_deg	7.268
r_rigid_bond_restr	3.339
r_angle_refined_deg	1.648
r_lrange_it	1.263
r_lrange_other	1.197
r_scangle_it	0.774
r_scangle_other	0.77
r_mcangle_it	0.696
r_mcangle_other	0.696
r_angle_other_deg	0.567
r_scbond_it	0.552
r_scbond_other	0.549
r_mcbond_it	0.474
r_mcbond_other	0.474
r_nbd_refined	0.25
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.18
r_nbd_other	0.158
r_xyhbond_nbd_refined	0.126
r_symmetry_nbd_refined	0.104
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.082
r_metal_ion_refined	0.076
r_symmetry_xyhbond_nbd_other	0.033
r_gen_planes_refined	0.011
r_bond_refined_d	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	4341
Nucleic Acid Atoms
Solvent Atoms	540
Heterogen Atoms	42

Software

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