3KOG | pdb_00003kog

Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.43	293	31.6000% 2-methyl-2,4-pentanediol, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.43, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.796	α = 90
b = 70.337	β = 90
c = 104.1	γ = 90

Symmetry
Space Group	I 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)	2009-06-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.85503,0.97926,0.97845	SSRL	BL11-1

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	1.85	29.814	100	0.091	0.091	10.2	4.1		21313			21.528

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	1.85	1.9	100		0.726	0.726	1	4.1	1549

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	1.85	29.814	21310	1095	99.99	0.184	0.182	0.19	0.214	0.23	RANDOM	18.402

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]
-0.25			-0.07		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.549
r_dihedral_angle_4_deg	17.383
r_dihedral_angle_3_deg	14.076
r_dihedral_angle_1_deg	6.642
r_scangle_it	4.3
r_scbond_it	2.69
r_mcangle_it	1.697
r_angle_refined_deg	1.621
r_mcbond_it	0.959
r_angle_other_deg	0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.549
r_dihedral_angle_4_deg	17.383
r_dihedral_angle_3_deg	14.076
r_dihedral_angle_1_deg	6.642
r_scangle_it	4.3
r_scbond_it	2.69
r_mcangle_it	1.697
r_angle_refined_deg	1.621
r_mcbond_it	0.959
r_angle_other_deg	0.93
r_mcbond_other	0.277
r_chiral_restr	0.102
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1729
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.