5G4Y

Structural basis for carboxylic acid recognition by a Cache chemosensory domain.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K08 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293PROTEIN AT 8.5 MG/ML IN 50 MM BIS-TRIS CHLORIDE, PH 6.5, 50 MM SODIUM CHLORIDE IN EQUAL VOLUME WITH 27% PEG 4000 AND 100 MM PROLINE AT 20 C IN SITTING DROPS.
Crystal Properties
Matthews coefficientSolvent content
3.6166

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.282α = 90
b = 74.282β = 90
c = 75.057γ = 120
Symmetry
Space GroupP 64

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2015-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1248.899.80.1114.211.216085
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0597.80.762.910.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4K08264.331521784099.980.161960.16070.18315RANDOM36.557
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]
1.520.761.52-4.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.373
r_dihedral_angle_4_deg15.144
r_dihedral_angle_3_deg13.442
r_dihedral_angle_1_deg6.412
r_mcangle_it4.443
r_scbond_it4.12
r_mcbond_other3.402
r_mcbond_it3.4
r_angle_refined_deg1.857
r_angle_other_deg1.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.373
r_dihedral_angle_4_deg15.144
r_dihedral_angle_3_deg13.442
r_dihedral_angle_1_deg6.412
r_mcangle_it4.443
r_scbond_it4.12
r_mcbond_other3.402
r_mcbond_it3.4
r_angle_refined_deg1.857
r_angle_other_deg1.043
r_chiral_restr0.119
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1167
Nucleic Acid Atoms
Solvent Atoms81
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing