8IUA

Crystal structure of GH66 endodextranase 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	100mM Tris-HCl, pH 8.5-9.0, 200mM lithium sulfate, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.712	α = 90
b = 47.996	β = 104.64
c = 76.477	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		2022-03-05	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	1.8	46.9	99.7	0.121	0.144	0.077	0.997	11	6.7		50250

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	1.8	1.84			0.92	1.085	0.57	0.839	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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	46.9	50249	2536	99.679	0.21	0.2083	0.2527	28.622

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]
-1.337		0.696	0.752		0.195

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.051
r_dihedral_angle_3_deg	14.477
r_dihedral_angle_1_deg	7.8
r_lrange_other	5.62
r_lrange_it	5.608
r_dihedral_angle_2_deg	4.314
r_angle_refined_deg	1.501
r_scangle_it	1.369
r_scangle_other	1.369
r_mcangle_it	0.975
r_mcangle_other	0.975
r_scbond_other	0.917
r_scbond_it	0.915
r_mcbond_it	0.707
r_mcbond_other	0.707
r_angle_other_deg	0.51
r_nbd_refined	0.225
r_symmetry_nbd_other	0.203
r_nbd_other	0.19
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_refined	0.11
r_metal_ion_refined	0.086
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.073
r_symmetry_nbd_refined	0.065
r_symmetry_xyhbond_nbd_other	0.012
r_gen_planes_refined	0.01
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4398
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	36

Software

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