7ZGZ | pdb_00007zgz

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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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
2.48	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	0.21	0.2442	0.25	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