7ZDY

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

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JP0	5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental model	PDB	5Z9S	5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental model	PDB	5YOT	5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental model	PDB	3U4A	5JP0, 5Z9S, 5YOT, 3U4A, 5XXL
experimental model	PDB	5XXL	5JP0, 5Z9S, 5YOT, 3U4A, 5XXL

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