8IU9 | pdb_00008iu9

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	ABQ07435.1

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
2.15	42.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.181	α = 90
b = 48.381	β = 104.405
c = 76.487	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	47.26	98.3	0.132	0.156	0.083	0.997	10.3	6.7		50429

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			0.963	1.133	0.591	0.854	2.1

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	47.256	50428	2464	98.258	0.209	0.2061	0.22	0.2593	0.27	27.053

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]
2.111		1.288	-0.833		-1.714

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.033
r_dihedral_angle_3_deg	14.967
r_dihedral_angle_2_deg	12.146
r_dihedral_angle_1_deg	7.964
r_lrange_other	4.486
r_lrange_it	4.483
r_scangle_it	2.508
r_scangle_other	2.507
r_angle_refined_deg	2.165
r_scbond_it	1.682
r_scbond_other	1.682
r_mcangle_it	1.532
r_mcangle_other	1.532
r_mcbond_it	1.049
r_mcbond_other	1.049
r_angle_other_deg	0.72
r_nbd_refined	0.215
r_nbd_other	0.208
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.106
r_symmetry_nbd_refined	0.093
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_other	0.022
r_gen_planes_refined	0.016
r_bond_refined_d	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4353
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	37

Software

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