7W0W

The novel membrane-proximal sensing mechanism in a broad-ligand binding chemoreceptor McpA of Bacillus velezensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6PXY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.17 M ammonium acetate, 0.085M sodium acetate pH 4.6, 25.5 % PEG 4000, 15 % glycerol

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 180.161α = 90
b = 32.855β = 90
c = 57.903γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97918SSRFBL17U1

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
12.2475099.70.09120.47.817195
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)
12.252.290.477

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6pxy2.24748.7561715087099.5470.1850.18250.236747.448
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]
-0.827-3.4384.265
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.798
r_dihedral_angle_4_deg17.591
r_dihedral_angle_3_deg14.955
r_lrange_other9.157
r_lrange_it9.155
r_scangle_it7.516
r_scangle_other7.514
r_dihedral_angle_1_deg6.83
r_mcangle_it5.134
r_mcangle_other5.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.798
r_dihedral_angle_4_deg17.591
r_dihedral_angle_3_deg14.955
r_lrange_other9.157
r_lrange_it9.155
r_scangle_it7.516
r_scangle_other7.514
r_dihedral_angle_1_deg6.83
r_mcangle_it5.134
r_mcangle_other5.133
r_scbond_it4.912
r_scbond_other4.911
r_mcbond_it3.744
r_mcbond_other3.73
r_angle_refined_deg1.47
r_angle_other_deg1.276
r_nbd_refined0.195
r_symmetry_xyhbond_nbd_refined0.185
r_symmetry_nbd_other0.17
r_nbd_other0.166
r_nbtor_refined0.163
r_xyhbond_nbd_refined0.15
r_ncsr_local_group_10.118
r_symmetry_nbd_refined0.098
r_symmetry_nbtor_other0.076
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2299
Nucleic Acid Atoms
Solvent Atoms107
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing