2VU6

Atomic resolution (0.95 A) structure of purified Thaumatin I grown in sodium meso-tartrate at 19 C.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.3292MICROBATCH METHOD; PROTEIN AT 26 MG/ML IN 10MM SODIUM PHOSPHATE WITH 62.5 MM SODIUM MESO-TARTRATE (PH=7.3) AND 2.5% (V/V) GLYCEROL; CRYSTALS GROWN AT 19 C.
Crystal Properties
Matthews coefficientSolvent content
1.729

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.886α = 90
b = 54.522β = 90
c = 70.872γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL FOCUSING MIRROR2008-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6ANSLSX6A

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
10.951299.50.0629.85.91239412
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
10.950.971005.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT0.9511.8511758462081000.1180.1170.136RANDOM8.39
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]
0.310.11-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.361
r_dihedral_angle_4_deg15.733
r_dihedral_angle_3_deg10.905
r_dihedral_angle_1_deg6.704
r_scangle_it4.479
r_scbond_it3.625
r_mcangle_it2.781
r_mcbond_it2.296
r_angle_refined_deg1.961
r_angle_other_deg1.037
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.361
r_dihedral_angle_4_deg15.733
r_dihedral_angle_3_deg10.905
r_dihedral_angle_1_deg6.704
r_scangle_it4.479
r_scbond_it3.625
r_mcangle_it2.781
r_mcbond_it2.296
r_angle_refined_deg1.961
r_angle_other_deg1.037
r_nbd_refined0.379
r_symmetry_vdw_other0.366
r_symmetry_vdw_refined0.239
r_nbd_other0.196
r_symmetry_hbond_refined0.188
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.181
r_chiral_restr0.125
r_nbtor_other0.092
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.004
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms1551
Nucleic Acid Atoms
Solvent Atoms341
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing