5Z8P

Structural basis for specific inhibition of highly sensitive ShHTL7 receptor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CBK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1 M MES monohydrate pH 6.5, 1.6 M Magnesium sulfate heptahydrate
Crystal Properties
Matthews coefficientSolvent content
3.1961.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.59α = 90
b = 92.59β = 90
c = 80.36γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.987SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.3540.0999.610.99923.129.185478
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.351.3980.575

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 REPLACEMENTTHROUGHOUT5CBK1.3540.0981206427499.70.129130.128350.14379RANDOM20.335
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]
-0.25-0.13-0.250.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.777
r_sphericity_free31.612
r_dihedral_angle_4_deg20.065
r_dihedral_angle_3_deg11.16
r_sphericity_bonded9.948
r_dihedral_angle_1_deg5.779
r_long_range_B_refined3.965
r_long_range_B_other2.763
r_scangle_other2.301
r_rigid_bond_restr1.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.777
r_sphericity_free31.612
r_dihedral_angle_4_deg20.065
r_dihedral_angle_3_deg11.16
r_sphericity_bonded9.948
r_dihedral_angle_1_deg5.779
r_long_range_B_refined3.965
r_long_range_B_other2.763
r_scangle_other2.301
r_rigid_bond_restr1.77
r_scbond_it1.735
r_scbond_other1.722
r_mcangle_other1.484
r_mcangle_it1.475
r_angle_refined_deg1.398
r_mcbond_it1.085
r_mcbond_other1.061
r_angle_other_deg0.847
r_chiral_restr0.088
r_bond_refined_d0.009
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2088
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
SCALAdata scaling
MOLREPphasing