3A0U | pdb_00003a0u

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3A10

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9.5	293	40% PEG600, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2	38.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.978	α = 90
b = 32.978	β = 90
c = 196.968	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		2005-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0	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	1.66	50	98	0.046	31.6	4.1		13692		-3	16.9

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)
	1.66	1.72	94		0.111	6.9	3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	3A10	1.66	20	13625	685	98.49	0.191	0.189	0.19	0.24	0.23	RANDOM	16.163

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]
-0.04			-0.04		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.118
r_dihedral_angle_4_deg	16.207
r_dihedral_angle_3_deg	11.567
r_dihedral_angle_1_deg	5.937
r_scangle_it	4.17
r_scbond_it	2.622
r_angle_refined_deg	1.591
r_mcangle_it	1.568
r_mcbond_it	1.023
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.118
r_dihedral_angle_4_deg	16.207
r_dihedral_angle_3_deg	11.567
r_dihedral_angle_1_deg	5.937
r_scangle_it	4.17
r_scbond_it	2.622
r_angle_refined_deg	1.591
r_mcangle_it	1.568
r_mcbond_it	1.023
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.207
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.15
r_metal_ion_refined	0.105
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	966
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	44

Software

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