3A0Z

Catalytic domain of histidine kinase ThkA (TM1359) (nucleotide free form 4: isopropanol, orthorombic)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3A0W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.629320% isopropanol, 0.1M sodium citrate, 20% PEG4000, pH 5.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.31α = 90
b = 61.094β = 90
c = 89.952γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102007-06-01MSINGLE 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
11.7550960.04429.5531968-319.1
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)
1.751.8186.30.2452.72.9

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 REPLACEMENTTHROUGHOUT3A0W1.7530.7731940162195.990.1980.1950.241RANDOM20.355
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]
0.03-0.590.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.04
r_dihedral_angle_4_deg15.521
r_dihedral_angle_3_deg14.525
r_dihedral_angle_1_deg6.783
r_scangle_it3.545
r_scbond_it2.419
r_mcangle_it1.574
r_angle_refined_deg1.417
r_mcbond_it0.99
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.04
r_dihedral_angle_4_deg15.521
r_dihedral_angle_3_deg14.525
r_dihedral_angle_1_deg6.783
r_scangle_it3.545
r_scbond_it2.419
r_mcangle_it1.574
r_angle_refined_deg1.417
r_mcbond_it0.99
r_nbtor_refined0.312
r_nbd_refined0.207
r_symmetry_hbond_refined0.172
r_symmetry_vdw_refined0.153
r_xyhbond_nbd_refined0.147
r_chiral_restr0.099
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2538
Nucleic Acid Atoms
Solvent Atoms292
Heterogen Atoms

Software

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