3K1U

Beta-xylosidase, family 43 glycosyl hydrolase from Clostridium acetobutylicum

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 M magnesium chloride, 0.1 M Hepes buffer, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.45	α = 90
b = 59.658	β = 90
c = 112.391	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315		2008-03-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.55	37.2	99.9	0.091	10.7	6.7	47116	47116			24.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	99		0.596	2.17	4.2	2299

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.55	37.2	47035	47035	2379	99.81	0.137	0.137	0.136	0.161	RANDOM	11.268

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]
-0.54			0.12		0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_3_deg	12.838
r_dihedral_angle_4_deg	11.424
r_dihedral_angle_1_deg	6.53
r_scangle_it	4.047
r_scbond_it	2.619
r_angle_refined_deg	1.819
r_mcangle_it	1.577
r_angle_other_deg	1.05
r_mcbond_it	0.963

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.215
r_dihedral_angle_3_deg	12.838
r_dihedral_angle_4_deg	11.424
r_dihedral_angle_1_deg	6.53
r_scangle_it	4.047
r_scbond_it	2.619
r_angle_refined_deg	1.819
r_mcangle_it	1.577
r_angle_other_deg	1.05
r_mcbond_it	0.963
r_mcbond_other	0.329
r_chiral_restr	0.128
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2583
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	36

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.