Experiment: 4FT8

E. coli Catabolite Activator Protein with Cobalt and Sulfate Ligands

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZRC	search 1: 1ZRC CAP N-terminal domain dimer; searches 2,3: 1ZRC CAP individual C-terminal domain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	A CAP-DNA complex was screened by hanging-drop vapor diffusion with Hampton Research Crystal Screens and pregreased VDX plates. Optimization of Crystal Screen 2 condition #25 yielded ruby-red colored crystals appearing within 3 days at 20 C in 0.01 M CoCl2.6H2O, 0.1 M MES monohydrate pH 6.5 and 2.5 M (NH4)2SO4. The crystallization process yielded crystals containing only CAP protein without DNA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.143	α = 90
b = 108.452	β = 90
c = 44.32	γ = 90

Symmetry
Space Group	P 21 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	108	CCD	ADSC QUANTUM 4		2007-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.07	NSLS	X8C

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	1.96	50	97.1	0.088	9.5	5.1	35645	35645

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	1.96	2.03	90.5		0.778		4.2	3280

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	MOLECULAR REPLACEMENT	search 1: 1ZRC CAP N-terminal domain dimer; searches 2,3: 1ZRC CAP individual C-terminal domain	1.966	40.781	1.34	35645	35596	1774	97.3	0.1977	0.1959	0.1955	0.23	0.2298	random	35.2859

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]
0.6641			-0.4729		-0.1912

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.888
f_angle_deg	1
f_bond_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3163
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	111

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
PHASER	phasing