3A0T

Catalytic domain of histidine kinase ThkA (TM1359) in complex with ADP and Mg ion (trigonal)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
othernucleotide free structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2935% isopropanol, 2.0M ammonium sulphate, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9568.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.943α = 90
b = 72.943β = 90
c = 91.258γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.0SPring-8BL44B2

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
11.91501000.04951.612.122342-324.8
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)
11.911.981000.432611.8

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 DIFFRACTIONTHROUGHOUTnucleotide free structure1.912022252113399.990.1860.1850.213RANDOM26.301
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]
0.150.080.15-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.697
r_dihedral_angle_3_deg17.443
r_dihedral_angle_4_deg15.472
r_scangle_it9.267
r_dihedral_angle_1_deg6.769
r_scbond_it6.164
r_mcangle_it4.258
r_mcbond_it3.306
r_angle_refined_deg1.93
r_nbtor_refined0.339
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.697
r_dihedral_angle_3_deg17.443
r_dihedral_angle_4_deg15.472
r_scangle_it9.267
r_dihedral_angle_1_deg6.769
r_scbond_it6.164
r_mcangle_it4.258
r_mcbond_it3.306
r_angle_refined_deg1.93
r_nbtor_refined0.339
r_nbd_refined0.328
r_symmetry_vdw_refined0.239
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.115
r_chiral_restr0.106
r_gen_planes_refined0.013
r_bond_refined_d0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1246
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms28

Software

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