8C7F

Crystal structure of beta-xylosidase mutant (D281N, E517Q) from Thermotoga maritima in complex with xylopentaose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ZEQ

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
2.55	51.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.35	α = 90
b = 100.89	β = 90
c = 179.11	γ = 90

Symmetry
Space Group	P 21 2 21

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		2022-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.52	50.445	99.9	0.097	0.114	0.06	0.999	9.6	6.9		272231

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.52	1.55			0.03	0.036	0.019	0.999		6.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.52	50.445	272165	13593	99.807	0.166	0.1643	0.1885	20.402

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]
1.08			0.083		-1.163

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.391
r_dihedral_angle_3_deg	13.562
r_dihedral_angle_2_deg	7.781
r_dihedral_angle_1_deg	6.889
r_lrange_it	5.701
r_lrange_other	5.701
r_scangle_it	4.669
r_scangle_other	4.668
r_scbond_it	3.156
r_scbond_other	3.156
r_mcangle_it	2.215
r_mcangle_other	2.215
r_mcbond_it	1.693
r_mcbond_other	1.691
r_angle_refined_deg	1.591
r_angle_other_deg	0.526
r_symmetry_nbd_refined	0.275
r_nbd_refined	0.217
r_nbd_other	0.197
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.14
r_symmetry_xyhbond_nbd_refined	0.127
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_1	0.061
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11751
Nucleic Acid Atoms
Solvent Atoms	1322
Heterogen Atoms	81

Software

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