6DB1

2.0 Angstrom Resolution Crystal Structure of N-Terminal Ligand-Binding Domain of Putative Methyl-Accepting Chemotaxis Protein from Salmonella enterica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8292Protein: 7.0 mg/ml, 0.01M Tris HCl (pH 8.3), ATP, Mg, Screen: PACT (C5), 0.1 PCB buffer (pH 8.0), 25% (w/v) PEG 1500
Crystal Properties
Matthews coefficientSolvent content
2.1342

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.226α = 90
b = 89.226β = 90
c = 65.89γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-10-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
123099.80.0750.0750.0840.03628.95.620259-339.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.031000.8260.8260.9260.4150.7182.044.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT229.2119193103699.720.224380.222180.26448RANDOM52.644
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]
-1.82-0.91-1.825.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.185
r_dihedral_angle_3_deg11.449
r_dihedral_angle_4_deg9.993
r_long_range_B_refined6.682
r_long_range_B_other6.678
r_scangle_other3.963
r_mcangle_it3.252
r_mcangle_other3.252
r_scbond_it2.536
r_scbond_other2.523
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.185
r_dihedral_angle_3_deg11.449
r_dihedral_angle_4_deg9.993
r_long_range_B_refined6.682
r_long_range_B_other6.678
r_scangle_other3.963
r_mcangle_it3.252
r_mcangle_other3.252
r_scbond_it2.536
r_scbond_other2.523
r_dihedral_angle_1_deg2.211
r_mcbond_it2.112
r_mcbond_other2.111
r_angle_refined_deg1.361
r_angle_other_deg0.476
r_chiral_restr0.066
r_gen_planes_refined0.023
r_gen_planes_other0.021
r_bond_refined_d0.008
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2109
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing