3OSD | pdb_00003osd

Crystal structure of a putative glycosyl hydrolase (BT2157) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.80 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	277	0.2M K3Citrate, 20.0% PEG-3350, No Buffer pH 8.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.11	60.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.42	α = 90
b = 87.42	β = 90
c = 97.182	γ = 90

Symmetry
Space Group	P 43 21 2

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 collimating mirror, toroid focusing mirror	2010-07-22	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97918,0.97903	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	29.454	99.4	0.082	14.3	5.8	35272	35272			23.083

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	99		0.802	0.802	2.1	5.9	2555

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.8	29.454	35247	1769	99.22	0.1607	0.1595	0.17	0.1836	0.19	RANDOM	31.9631

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]
0.36			0.36		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.294
r_dihedral_angle_4_deg	16.415
r_dihedral_angle_3_deg	12.065
r_dihedral_angle_1_deg	7
r_scangle_it	3.237
r_scbond_it	2.123
r_angle_refined_deg	1.408
r_mcangle_it	1.313
r_angle_other_deg	0.856
r_mcbond_it	0.736

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.294
r_dihedral_angle_4_deg	16.415
r_dihedral_angle_3_deg	12.065
r_dihedral_angle_1_deg	7
r_scangle_it	3.237
r_scbond_it	2.123
r_angle_refined_deg	1.408
r_mcangle_it	1.313
r_angle_other_deg	0.856
r_mcbond_it	0.736
r_mcbond_other	0.207
r_chiral_restr	0.096
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2084
Nucleic Acid Atoms
Solvent Atoms	395
Heterogen Atoms	46

Software

Software
Software Name	Purpose
SHELX	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	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 R01GM157729.