Experiment: 4EV0

Crystal Structure of Thermus thermophilus Catabolite Activator Protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PQQ	Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw
experimental model	PDB	3D0S	Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw
experimental model	PDB	3H3U	Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw
experimental model	PDB	2ZCW	Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	Screening for crystallization used the Gryphon liquid handling system (Art Robbins Instruments). Crystals were grown using sitting drops (200 nL protein + 200 nL crystallization reagent) with 60 UL reservoirs of crystallization reagent in a 96-well high-throughput screen. Plate-shaped crystals were obtained at 20 degree C using Hampton Research NATRIX HT #38: 0.2 M ammonium acetate, 0.15 M magnesium acetate tetrahydrate, 5% (w/v) polyethylene glycol 4000, and 0.05 M HEPES sodium, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.25	α = 90
b = 94.842	β = 90
c = 121.439	γ = 90

Symmetry
Space Group	P 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	ADSC QUANTUM 315		2010-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

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	2.4	100	93.9	0.08	13.9	24.5	20242	20242			43

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	2.4	2.44	50.6		0.565		6.5	535

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	THROUGHOUT	Nterminal domain: composite model of pruned fragments from PDB entries 2pqq, 3d0s, 3h3u representing residues 21-102; C-terminal domain: pruned fragment from PDB entry 2zcw	2.402	44.173	1.34	20242	20187	1031	93.67	0.2028	0.2	0.2007	0.2555	0.2591	5% randomly selected	64.9012

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]
28.9091			-15.1925		-13.7167

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.071
f_angle_d	1.165
f_chiral_restr	0.073
f_bond_d	0.008
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3328
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	70

Software

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