3H5I

Crystal structure of the N-terminal domain of a response regulator/sensory box/GGDEF 3-domain protein from Carboxydothermus hydrogenoformans

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	294	100mM Hepes pH 8.5, 4.2M sodium chloride, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.668	α = 90
b = 86.668	β = 90
c = 131.156	γ = 120

Symmetry
Space Group	H 3 2

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	MAR CCD 165 mm		2009-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.9	65.144	99.9	0.106	0.106	14.7	12.4	15201	15186			26

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)
	1.9	2	100		0.681	0.681	4.1	12.5	2176

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.9	20	15188	15174	762	99.91	0.213	0.212	0.238	RANDOM	35.116

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]
-0.58	-0.29		-0.58		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.135
r_dihedral_angle_4_deg	25.051
r_dihedral_angle_3_deg	14.236
r_dihedral_angle_1_deg	5.718
r_scangle_it	4.689
r_scbond_it	2.828
r_mcangle_it	2.013
r_angle_refined_deg	1.444
r_mcbond_it	1.063
r_angle_other_deg	0.895

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.135
r_dihedral_angle_4_deg	25.051
r_dihedral_angle_3_deg	14.236
r_dihedral_angle_1_deg	5.718
r_scangle_it	4.689
r_scbond_it	2.828
r_mcangle_it	2.013
r_angle_refined_deg	1.444
r_mcbond_it	1.063
r_angle_other_deg	0.895
r_mcbond_other	0.243
r_chiral_restr	0.083
r_bond_refined_d	0.016
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	961
Nucleic Acid Atoms
Solvent Atoms	22
Heterogen Atoms	2

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	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.