6FJ8

Structure of Thaumatin collected from an in situ crystal collected on ID30B at 12.7 keV.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A47 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1M HEPES and 0.7 M potassium/sodium tartrate
Crystal Properties
Matthews coefficientSolvent content
3.0559.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.569α = 90
b = 58.569β = 90
c = 151.584γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELDECTRIS PILATUS3 6MBe CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing)2016-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9763ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.554.6498.20.1070.1420.0710.995.73.64212415.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5398.40.9311.370.7120.3913.5

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 REPLACEMENTTHROUGHOUT5a471.554.6339983213097.450.131740.12990.16688RANDOM22.094
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]
-0.36-0.360.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.148
r_sphericity_free24.942
r_dihedral_angle_4_deg13.545
r_dihedral_angle_3_deg12.41
r_sphericity_bonded12.379
r_dihedral_angle_1_deg9.863
r_long_range_B_refined3.345
r_long_range_B_other3.266
r_scangle_other2.961
r_scbond_other2.366
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.148
r_sphericity_free24.942
r_dihedral_angle_4_deg13.545
r_dihedral_angle_3_deg12.41
r_sphericity_bonded12.379
r_dihedral_angle_1_deg9.863
r_long_range_B_refined3.345
r_long_range_B_other3.266
r_scangle_other2.961
r_scbond_other2.366
r_scbond_it2.362
r_rigid_bond_restr2.345
r_mcangle_other2.252
r_mcangle_it2.226
r_mcbond_it1.666
r_mcbond_other1.596
r_angle_refined_deg1.565
r_angle_other_deg0.977
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.002
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 Atoms1545
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing