3A0U

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)
TypeSourceAccession CodeDetails
experimental modelPDB 3A10 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION9.529340% PEG600, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
238.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.978α = 90
b = 32.978β = 90
c = 196.968γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 2102005-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.0SPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6650980.04631.64.113692-316.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.661.72940.1116.93

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3A101.66201362568598.490.1910.1890.24RANDOM16.163
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]
-0.04-0.040.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.118
r_dihedral_angle_4_deg16.207
r_dihedral_angle_3_deg11.567
r_dihedral_angle_1_deg5.937
r_scangle_it4.17
r_scbond_it2.622
r_angle_refined_deg1.591
r_mcangle_it1.568
r_mcbond_it1.023
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.118
r_dihedral_angle_4_deg16.207
r_dihedral_angle_3_deg11.567
r_dihedral_angle_1_deg5.937
r_scangle_it4.17
r_scbond_it2.622
r_angle_refined_deg1.591
r_mcangle_it1.568
r_mcbond_it1.023
r_nbtor_refined0.311
r_symmetry_vdw_refined0.242
r_nbd_refined0.207
r_symmetry_hbond_refined0.151
r_xyhbond_nbd_refined0.15
r_metal_ion_refined0.105
r_chiral_restr0.091
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms966
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing