3K6Q | pdb_00003k6q

CRYSTAL STRUCTURE OF An antitoxin part of a putative toxin/antitoxin system (SWOL_0700) FROM SYNTROPHOMONAS WOLFEI SUBSP. WOLFEI AT 1.80 A RESOLUTION

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	277	0.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.974	α = 107
b = 56.943	β = 103.03
c = 62.561	γ = 100.21

Symmetry
Space Group	P 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	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2009-06-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97905,0.97860	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	1.8	29.828	97	0.048	0.048	10.8	2		46885			24.57

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	95.9		0.344	0.344	2.2	2	3459

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	29.828	46885	2379	97.05	0.195	0.193	0.21	0.249	0.26	RANDOM	19.112

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]
-0.09	-1.45	0.35	-0.45	-0.82	-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.441
r_dihedral_angle_4_deg	19.699
r_dihedral_angle_3_deg	15.085
r_dihedral_angle_1_deg	6.459
r_scangle_it	3.901
r_scbond_it	2.452
r_mcangle_it	1.627
r_angle_refined_deg	1.545
r_angle_other_deg	0.937
r_mcbond_it	0.925

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.441
r_dihedral_angle_4_deg	19.699
r_dihedral_angle_3_deg	15.085
r_dihedral_angle_1_deg	6.459
r_scangle_it	3.901
r_scbond_it	2.452
r_mcangle_it	1.627
r_angle_refined_deg	1.545
r_angle_other_deg	0.937
r_mcbond_it	0.925
r_mcbond_other	0.255
r_chiral_restr	0.098
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4509
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
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.