3T4K

Arabidopsis histidine kinase 4 sensor domain in complex with N-benzyladenine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3T4J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529816% PEG 3,350, 0.2 M Na malonate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5351.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.14α = 90
b = 60.14β = 90
c = 297.52γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.10.99988ALS8.2.1

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
11.7746.1199.40.08917.0210.86205062050-3-3
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)
11.771.8291.60.4952.86.94122

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3T4J1.7746.115894158941310799.370.181540.181540.180040.20963RANDOM21.828
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]
0.840.420.84-1.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.62
r_dihedral_angle_4_deg13.199
r_dihedral_angle_3_deg13.132
r_dihedral_angle_1_deg5.657
r_scangle_it2.909
r_scbond_it1.836
r_angle_refined_deg1.386
r_mcangle_it1.158
r_angle_other_deg0.932
r_mcbond_it0.674
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.62
r_dihedral_angle_4_deg13.199
r_dihedral_angle_3_deg13.132
r_dihedral_angle_1_deg5.657
r_scangle_it2.909
r_scbond_it1.836
r_angle_refined_deg1.386
r_mcangle_it1.158
r_angle_other_deg0.932
r_mcbond_it0.674
r_mcbond_other0.204
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4226
Nucleic Acid Atoms
Solvent Atoms514
Heterogen Atoms41

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling