3S5Q

Crystal structure of a putative glycosyl hydrolase (BDI_2473) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	0.200M NH4I, 20.00% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.062	α = 90
b = 60.473	β = 90
c = 77.221	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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)	2009-07-07	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97954,0.91837,0.97874	SSRL	BL11-1

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	1.85	36.25	97.1	0.097	11.41	3.98		16569		-3	20.25

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	1.85	1.92	96.1		0.683	2.1	3.99

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	1.85	36.25	16554	854	97.26	0.1711	0.1693	0.2018	RANDOM	25.9466

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]
2.38			-1.43		-0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.407
r_dihedral_angle_4_deg	13.915
r_dihedral_angle_3_deg	13.653
r_dihedral_angle_1_deg	6.822
r_scangle_it	3.214
r_scbond_it	2.162
r_angle_refined_deg	1.529
r_mcangle_it	1.289
r_angle_other_deg	0.895
r_mcbond_it	0.764

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.407
r_dihedral_angle_4_deg	13.915
r_dihedral_angle_3_deg	13.653
r_dihedral_angle_1_deg	6.822
r_scangle_it	3.214
r_scbond_it	2.162
r_angle_refined_deg	1.529
r_mcangle_it	1.289
r_angle_other_deg	0.895
r_mcbond_it	0.764
r_mcbond_other	0.221
r_chiral_restr	0.093
r_bond_refined_d	0.017
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	1728
Nucleic Acid Atoms
Solvent Atoms	187
Heterogen Atoms	27

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
autoSHARP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.