6ZIV

Crystal structure of a Beta-glucosidase from Alicyclobacillus acidiphilus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	condition H3 (0.1 M Bis-Tris pH 5.5 and 25% (w/v) PEG3350) from the JCSG screen (Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
2.86	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.654	α = 91.616
b = 91.644	β = 90.422
c = 159.342	γ = 89.988

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2019-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.9139	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.55	159.2743	91.1	0.098	0.996	9	84.9		367007

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.64			0.561	0.608

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	FREE R-VALUE	sequence	1.95	46.55	247956	24694	95.977	0.266	0.2622	0.2963	11.898

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]
-0.37	0.05	-0.046	0.268	0.119	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.117
r_dihedral_angle_4_deg	18.34
r_dihedral_angle_3_deg	13.714
r_dihedral_angle_1_deg	6.268
r_lrange_it	4.389
r_scangle_it	1.414
r_mcangle_it	1.387
r_angle_refined_deg	1.31
r_scbond_it	0.937
r_mcbond_it	0.891
r_symmetry_nbd_refined	0.339
r_metal_ion_refined	0.327
r_nbtor_refined	0.316
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.231
r_symmetry_xyhbond_nbd_refined	0.225
r_chiral_restr	0.104
r_ncsr_local_group_7	0.1
r_ncsr_local_group_13	0.093
r_ncsr_local_group_27	0.092
r_ncsr_local_group_3	0.091
r_ncsr_local_group_6	0.091
r_ncsr_local_group_28	0.09
r_ncsr_local_group_25	0.088
r_ncsr_local_group_1	0.086
r_ncsr_local_group_2	0.086
r_ncsr_local_group_4	0.086
r_ncsr_local_group_5	0.086
r_ncsr_local_group_10	0.085
r_ncsr_local_group_24	0.085
r_ncsr_local_group_18	0.084
r_ncsr_local_group_23	0.083
r_ncsr_local_group_12	0.082
r_ncsr_local_group_26	0.08
r_ncsr_local_group_21	0.078
r_ncsr_local_group_22	0.078
r_ncsr_local_group_19	0.076
r_ncsr_local_group_8	0.075
r_ncsr_local_group_9	0.075
r_ncsr_local_group_11	0.074
r_ncsr_local_group_17	0.073
r_ncsr_local_group_16	0.071
r_ncsr_local_group_15	0.069
r_ncsr_local_group_20	0.069
r_ncsr_local_group_14	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28359
Nucleic Acid Atoms
Solvent Atoms	1952
Heterogen Atoms	189

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
STARANISO	data scaling
BALBES	phasing