4H08 | pdb_00004h08

Crystal structure of a putative hydrolase (BT3161) 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	5.6	277	5.00% Glycerol, 19.00% iso-Propanol, 19.00% PEG-4000, 0.1M Citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.89	α = 90
b = 77.89	β = 90
c = 64.094	γ = 120

Symmetry
Space Group	P 31 2 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	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2012-02-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97975,0.91162,0.97916	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	1.8	29.847	99.4	0.104	9.98			21120		-3	17.128

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	97.6		0.578	2

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	29.847	21100	1086	99.63	0.1496	0.1474	0.15	0.1901	0.19	RANDOM	17.6735

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]
0.3	0.15		0.3		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.197
r_dihedral_angle_4_deg	18.907
r_dihedral_angle_3_deg	10.956
r_dihedral_angle_1_deg	5.795
r_scangle_it	5.668
r_scbond_it	3.859
r_mcangle_it	2.307
r_mcbond_it	1.424
r_angle_refined_deg	1.315
r_angle_other_deg	0.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.197
r_dihedral_angle_4_deg	18.907
r_dihedral_angle_3_deg	10.956
r_dihedral_angle_1_deg	5.795
r_scangle_it	5.668
r_scbond_it	3.859
r_mcangle_it	2.307
r_mcbond_it	1.424
r_angle_refined_deg	1.315
r_angle_other_deg	0.91
r_mcbond_other	0.42
r_chiral_restr	0.09
r_bond_refined_d	0.013
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	1594
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	13

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 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.