8XUL | pdb_00008xul

Structure of beta-1,2-glucanase from Xanthomonas campestris pv. campestris (beta-1,2-glucoheptasaccharide complex)-E239Q mutant

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	NaNO3, PEG 3350, Bis-tris propane

Crystal Properties
Matthews coefficient	Solvent content
7.21	82.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.178	α = 90
b = 220.178	β = 90
c = 220.178	γ = 90

Symmetry
Space Group	P 43 3 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 PILATUS 6M		2022-02-05	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)	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	2.45	49.233	100	0.121	0.027	1	33.7	39.1		67208

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	2.45	2.51			1.05	0.233	0.949	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.5	49.233	63225	3168	99.896	0.339	0.3381	0.3421	0.3646	0.3678	41.267

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.365
r_dihedral_angle_6_deg	16.202
r_dihedral_angle_1_deg	7.088
r_lrange_it	6.194
r_lrange_other	6.194
r_dihedral_angle_2_deg	6.057
r_scangle_it	4.946
r_scangle_other	4.945
r_mcangle_other	4.495
r_mcangle_it	4.491
r_scbond_it	3.539
r_scbond_other	3.538
r_mcbond_it	3.141
r_mcbond_other	3.124
r_angle_refined_deg	2.011
r_angle_other_deg	0.822
r_nbd_refined	0.284
r_symmetry_nbd_other	0.216
r_symmetry_nbd_refined	0.208
r_nbtor_refined	0.193
r_xyhbond_nbd_refined	0.183
r_nbd_other	0.161
r_chiral_restr	0.146
r_symmetry_xyhbond_nbd_refined	0.11
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.059
r_gen_planes_other	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_chiral_restr_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3620
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	78

Software

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