7ZDY

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

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
2.52	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 178.62	α = 90
b = 97.68	β = 90
c = 100.69	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	1.46	51.25	100	1	64.2	13.1		302573

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	1.46	1.49			0.331

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	1.46	51.25	302502	15107	99.549	0.173	0.1717	0.1909	28.782

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]
-1.78			2.139		-0.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.709
r_dihedral_angle_4_deg	18.142
r_dihedral_angle_3_deg	12.989
r_dihedral_angle_1_deg	6.588
r_lrange_it	5.487
r_scangle_it	5.262
r_scbond_it	3.782
r_mcangle_it	2.657
r_mcbond_it	2.068
r_angle_refined_deg	1.743
r_nbtor_refined	0.319
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.142
r_chiral_restr	0.12
r_xyhbond_nbd_refined	0.1
r_ncsr_local_group_1	0.059
r_bond_refined_d	0.011
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11856
Nucleic Acid Atoms
Solvent Atoms	813
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing