8XUJ | pdb_00008xuj

Structure of beta-1,2-glucanase from Endozoicomonas elysicola (EeSGL1, ligand-free)

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	potassium thiocyanate, Bis-tris propane, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.502	α = 90
b = 114.908	β = 90
c = 78.885	γ = 90

Symmetry
Space Group	P 21 21 2

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 6M		2018-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.4	46.442	100	0.141	0.057	0.998	14.1	13.2		40027

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	100		0.932	0.372	0.888	2.9	13.9

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	2.4	46.442	39979	2102	99.962	0.227	0.2236	0.2269	0.2808	0.2817	45.488

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]
0.037			-0.016		-0.021

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.739
r_dihedral_angle_6_deg	14.489
r_dihedral_angle_2_deg	9.751
r_dihedral_angle_1_deg	7.397
r_lrange_it	7.332
r_lrange_other	7.332
r_scangle_it	5.432
r_scangle_other	5.432
r_mcangle_it	4.83
r_mcangle_other	4.829
r_scbond_it	3.431
r_scbond_other	3.43
r_mcbond_it	3.215
r_mcbond_other	3.215
r_angle_refined_deg	1.42
r_angle_other_deg	0.504
r_symmetry_nbd_refined	0.253
r_nbd_refined	0.231
r_symmetry_nbd_other	0.208
r_nbtor_refined	0.188
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.166
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.023
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6729
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms

Software

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