7ZGZ

Crystal structure of beta-xylosidase from Thermotoga maritima in complex with methyl-beta-D-xylopyranoside hydrolysed to xylose

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	293	3% polyethylene glycol 8000, 48% 2-methyl-2,4-pentanediol, 0.1 M sodium cacodylate pH 5.9

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.58	α = 90
b = 97.21	β = 90
c = 99.87	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	175	PIXEL	DECTRIS EIGER2 XE 16M		2020-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	54.923	99.6	0.999	67.8	13.1		147912

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.88			0.433

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	THROUGHOUT	5JP0, 5Z9S, 5YOT, 3U4A, 5XXL	1.85	54.923	147781	7499	99.529	0.206	0.2037	0.2442	45.489

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]
-4.742			2.876		1.866

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.308
r_dihedral_angle_4_deg	18.571
r_dihedral_angle_3_deg	14.555
r_dihedral_angle_1_deg	9.491
r_lrange_other	6.778
r_lrange_it	6.776
r_scangle_it	5.699
r_scangle_other	5.698
r_mcangle_it	4.205
r_mcangle_other	4.205
r_scbond_it	4.02
r_scbond_other	4.02
r_mcbond_it	3.245
r_mcbond_other	3.245
r_angle_refined_deg	1.477
r_angle_other_deg	1.271
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.179
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.167
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.13
r_nbd_other	0.13
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_1	0.072
r_chiral_restr	0.067
r_xyhbond_nbd_other	0.066
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11783
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing