8IU8 | pdb_00008iu8

Crystal structure of GH66 endodextranase from Flavobacterium johnsoniae

X-RAY DIFFRACTION

---

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
2.17	43.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.241	α = 90
b = 48.409	β = 104.601
c = 76.453	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	1.85	47.3	99.7	0.112	0.134	0.073	0.995	10.1	6.3		47439

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	1.85	1.89			0.875	1.033	0.546	0.87	1.9

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	1.85	47.3	47428	2332	99.637	0.177	0.1748	0.19	0.2304	0.24	32.254

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]
1.714		-0.286	-0.5		-0.938

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.138
r_dihedral_angle_3_deg	14.865
r_dihedral_angle_1_deg	8.294
r_lrange_it	5.783
r_lrange_other	5.766
r_dihedral_angle_2_deg	5.722
r_scangle_it	3.902
r_scangle_other	3.901
r_scbond_it	2.809
r_scbond_other	2.808
r_mcangle_it	2.546
r_mcangle_other	2.546
r_angle_refined_deg	2.151
r_mcbond_it	1.927
r_mcbond_other	1.926
r_angle_other_deg	0.748
r_nbd_refined	0.219
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.193
r_symmetry_nbd_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.168
r_nbd_other	0.159
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.089
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	4341
Nucleic Acid Atoms
Solvent Atoms	355
Heterogen Atoms	6

Software

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