3A10 | pdb_00003a10

Crystal structure of response regulator protein TrrA (TM1360) from Thermotoga maritima in complex with Mg(2+)-BeF (SeMet, L89M)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.2	293	50% PEG200, 0.1M sodium/potassium-phosphate, 0.1M sodium chloride, pH 6.2, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.678	α = 90
b = 32.678	β = 90
c = 199.242	γ = 90

Symmetry
Space Group	P 41 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	100	CCD	RIGAKU JUPITER 210		2006-03-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	0.9795,0.9797,0.9787	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.63	50	98.9	0.037	43.7	7.3		14298		-3	18.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.63	1.69	99.8		0.143	8.9	6.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.63	20	14289	719	98.69	0.203	0.2	0.2	0.25	0.24	RANDOM	19.765

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]
-0.17			-0.17		0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.869
r_dihedral_angle_4_deg	23.483
r_dihedral_angle_3_deg	12.655
r_dihedral_angle_1_deg	5.998
r_scangle_it	3.719
r_scbond_it	2.423
r_angle_refined_deg	1.446
r_mcangle_it	1.39
r_mcbond_it	1.002
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.869
r_dihedral_angle_4_deg	23.483
r_dihedral_angle_3_deg	12.655
r_dihedral_angle_1_deg	5.998
r_scangle_it	3.719
r_scbond_it	2.423
r_angle_refined_deg	1.446
r_mcangle_it	1.39
r_mcbond_it	1.002
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.21
r_symmetry_hbond_refined	0.144
r_xyhbond_nbd_refined	0.137
r_metal_ion_refined	0.097
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	968
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

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.