4QHX

Crystal structure of a putative two-domain sugar hydrolase (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	0.16M ammonium sulfate, 20.0% Glycerol, 20.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.042	α = 90
b = 110.042	β = 90
c = 105.557	γ = 120

Symmetry
Space Group	H 3

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	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2014-04-04	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.97934,0.95369,0.97913	SSRL	BL14-1

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	1.8	29.643	96.5	0.052	9.27			43818		-3	25.126

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	1.8	1.86	91.8		0.503	1.6

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	29.643	43818	2198	99.43	0.1507	0.1492	0.1789	RANDOM	29.4797

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]
0.51	0.25		0.51		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_4_deg	21.751
r_dihedral_angle_3_deg	12.412
r_dihedral_angle_1_deg	6.479
r_mcangle_it	1.741
r_angle_refined_deg	1.525
r_mcbond_it	1.198
r_mcbond_other	1.197
r_angle_other_deg	0.804
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_4_deg	21.751
r_dihedral_angle_3_deg	12.412
r_dihedral_angle_1_deg	6.479
r_mcangle_it	1.741
r_angle_refined_deg	1.525
r_mcbond_it	1.198
r_mcbond_other	1.197
r_angle_other_deg	0.804
r_chiral_restr	0.096
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3230
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	109

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	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.