3G6I

Crystal structure of an outer membrane protein, part of a putative carbohydrate binding complex (bt_1022) from bacteroides thetaiotaomicron vpi-5482 at 1.93 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.67	277	NANODROP, 0.25M Lithium sulfate, 34.0% PEG 4000, 0.1M Tris-HCl pH 8.67, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.85	68.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.025	α = 90
b = 75.025	β = 90
c = 127.29	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	2009-01-17	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837, 0.97964, 0.97949	SSRL	BL9-2

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	1.93	48.97	100	0.119	14.99	10.8		28120		-3	34.847

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	1.93	2	100		1.556	1.5

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	1.93	48.97	28048	1409	99.95	0.198	0.197	0.223	RANDOM	32.801

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]
0.67			0.67		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.245
r_dihedral_angle_4_deg	15.81
r_dihedral_angle_3_deg	14.609
r_scangle_it	7.634
r_scbond_it	5.149
r_dihedral_angle_1_deg	4.627
r_mcangle_it	2.891
r_mcbond_it	1.732
r_angle_refined_deg	1.37
r_angle_other_deg	0.917

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.245
r_dihedral_angle_4_deg	15.81
r_dihedral_angle_3_deg	14.609
r_scangle_it	7.634
r_scbond_it	5.149
r_dihedral_angle_1_deg	4.627
r_mcangle_it	2.891
r_mcbond_it	1.732
r_angle_refined_deg	1.37
r_angle_other_deg	0.917
r_mcbond_other	0.525
r_chiral_restr	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1585
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	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.