5AVG

The 0.95 angstrom structure of thaumatin crystallized in high-strength agarose hydrogel


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VHK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH72930.1 M Hepes-NaOH (pH 7.0), 0.33 M Na/K tartrate
Crystal Properties
Matthews coefficientSolvent content
2.8256.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.839α = 90
b = 57.839β = 90
c = 149.552γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2009-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

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
10.9553.9592.90.05421.57.5148780
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)
10.950.97560.352.252.3

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 REPLACEMENTTHROUGHOUT2VHK0.9553.95141256745592.980.12780.126950.14402RANDOM13.695
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]
0.240.24-0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.406
r_sphericity_free23.081
r_dihedral_angle_4_deg16.139
r_dihedral_angle_3_deg11.95
r_rigid_bond_restr7.456
r_dihedral_angle_1_deg7.098
r_sphericity_bonded6.854
r_long_range_B_refined3.182
r_long_range_B_other2.563
r_scangle_other2.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.406
r_sphericity_free23.081
r_dihedral_angle_4_deg16.139
r_dihedral_angle_3_deg11.95
r_rigid_bond_restr7.456
r_dihedral_angle_1_deg7.098
r_sphericity_bonded6.854
r_long_range_B_refined3.182
r_long_range_B_other2.563
r_scangle_other2.298
r_scbond_it2.242
r_scbond_other2.241
r_angle_refined_deg2.221
r_mcangle_it1.693
r_mcangle_other1.59
r_mcbond_it1.359
r_mcbond_other1.359
r_angle_other_deg1.024
r_chiral_restr0.154
r_bond_refined_d0.025
r_gen_planes_refined0.013
r_bond_other_d0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1546
Nucleic Acid Atoms
Solvent Atoms274
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing