3FX3

Structure of a putative cAMP-binding regulatory protein from Silicibacter pomeroyi DSS-3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	0.49M NaH2PO4, 0.91M K2HPO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.728	α = 90
b = 137.728	β = 90
c = 94.626	γ = 120

Symmetry
Space Group	H 3

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	CUSTOM-MADE		2007-12-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97926,0.97940	APS	19-BM

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	2.2	50	99.7	0.079	35.955	7	33872	33872		-3	44.6

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	2.2	2.25	99.7		0.491		6.5	2284

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.2	31.54	33749	33749	1713	99.31	0.183	0.183	0.181	0.218	RANDOM	36.656

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]
-1.26	-0.63		-1.26		1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.289
r_dihedral_angle_4_deg	19.959
r_dihedral_angle_3_deg	14.303
r_dihedral_angle_1_deg	5.784
r_scangle_it	3.862
r_scbond_it	2.414
r_angle_refined_deg	1.422
r_mcangle_it	1.396
r_angle_other_deg	0.882
r_mcbond_it	0.711

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.289
r_dihedral_angle_4_deg	19.959
r_dihedral_angle_3_deg	14.303
r_dihedral_angle_1_deg	5.784
r_scangle_it	3.862
r_scbond_it	2.414
r_angle_refined_deg	1.422
r_mcangle_it	1.396
r_angle_other_deg	0.882
r_mcbond_it	0.711
r_mcbond_other	0.182
r_chiral_restr	0.085
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3464
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	42

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.