4TVT

New ligand for thaumatin discovered using acoustic high throughput screening


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1THI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.62911.5M NaK Tartrate, 0.1M Bis Tris pH 6.6
Crystal Properties
Matthews coefficientSolvent content
2.8158

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.837α = 90
b = 57.837β = 90
c = 149.584γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

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
11.253.9589.830.02942.8114.66846168461
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)
11.21.2223.60.34711.7

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 REPLACEMENTTHROUGHOUT1THI1.253.9568461351889.830.14550.144610.16275RANDOM17.345
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]
0.360.36-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.249
r_dihedral_angle_4_deg22.777
r_dihedral_angle_1_deg12.149
r_dihedral_angle_3_deg12.018
r_long_range_B_refined10.048
r_long_range_B_other9.005
r_scangle_other5.745
r_scbond_other3.842
r_scbond_it3.836
r_angle_refined_deg2.867
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.249
r_dihedral_angle_4_deg22.777
r_dihedral_angle_1_deg12.149
r_dihedral_angle_3_deg12.018
r_long_range_B_refined10.048
r_long_range_B_other9.005
r_scangle_other5.745
r_scbond_other3.842
r_scbond_it3.836
r_angle_refined_deg2.867
r_mcangle_other2.419
r_mcangle_it2.394
r_mcbond_it1.623
r_mcbond_other1.578
r_angle_other_deg1.072
r_chiral_restr0.179
r_bond_refined_d0.033
r_gen_planes_refined0.013
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1551
Nucleic Acid Atoms
Solvent Atoms442
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement