3BO6 | pdb_00003bo6

Structure of the Chromobacterium violaceum VirA (SpvC) Phosphothreonine Lyase effector protein

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.8	287	1M ammonium sulphate, 0.1M BICINE, pH8.8, VAPOR DIFFUSION, HANGING DROP, temperature 287K
2	VAPOR DIFFUSION, HANGING DROP	8	287	1M ammonium sulphate, 0.1M Tris-HCl, pH8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.671	α = 90
b = 119.777	β = 105.63
c = 44.492	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2007-11-12	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2007-08-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.92	Diamond	I03
2	SYNCHROTRON	ESRF BEAMLINE BM14	0.97866, 0.97893, 0.88560	ESRF	BM14

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	1.4	59.888	87.9	0.077	0.077	6.8	3.4	75030	74121	6	6	10.2

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)
	1.4	1.48	75.8		0.307	0.307	2.1	1.8	9314

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.4	41.094	75030	71146	3514	84.38	0.1599	0.159	0.16	0.189	0.19	RANDOM	16.31

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]
2.247		-1.426	-1.65		-0.596

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.428
f_nbd_refined	4.114
f_angle_d	1.33
f_chiral_restr	0.083
f_bond_d	0.007
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3614
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	10

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
SHELX	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
SHELXCD	phasing
SHELXE	model building

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.