3E8V

Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	294	100mM sodium cacodylate pH 6.5, 1.4M sodium acetate hydrate, Vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.52	65.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.006	α = 90
b = 82.006	β = 90
c = 32.367	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	CCD	MAR CCD 165 mm		2008-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	19.699	99.9	0.1	0.1	30.1	22	5084	5079			51.6

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)
	2.4	2.53	99.8		0.574	0.574	5.8	22.3	737

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.4	15	5054	5050	224	99.92	0.226	0.225	0.243	RANDOM	36.837

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]
-1.07	-0.54		-1.07		1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.687
r_dihedral_angle_3_deg	17.773
r_dihedral_angle_1_deg	6.364
r_scangle_it	3.122
r_scbond_it	2.016
r_mcangle_it	1.708
r_angle_refined_deg	1.527
r_mcbond_it	0.924
r_symmetry_vdw_refined	0.436
r_metal_ion_refined	0.325

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.687
r_dihedral_angle_3_deg	17.773
r_dihedral_angle_1_deg	6.364
r_scangle_it	3.122
r_scbond_it	2.016
r_mcangle_it	1.708
r_angle_refined_deg	1.527
r_mcbond_it	0.924
r_symmetry_vdw_refined	0.436
r_metal_ion_refined	0.325
r_symmetry_metal_ion_refined	0.32
r_nbtor_refined	0.307
r_nbd_refined	0.241
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.09
r_symmetry_hbond_refined	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	600
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.