5YYQ

Structure K78A thaumatin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AL7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.1M ADA, 0.75M potassium sodium tartrate, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.8256.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.719α = 90
b = 57.719β = 90
c = 150.386γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2012-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B10.8SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.075099.90.0560.99971.2610.7112490
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.071.0999.80.4960.9648.210.6

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 REPLACEMENTFREE R-VALUE3al71.07201123851000.1330.1330.141RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
3714221844.1
RMS Deviations
KeyRefinement Restraint Deviation
s_approx_iso_adps0.1641
s_zero_chiral_vol0.0974
s_non_zero_chiral_vol0.0974
s_similar_adp_cmpnt0.0481
s_angle_d0.0351
s_anti_bump_dis_restr0.031
s_bond_d0.0173
s_rigid_bond_adp_cmpnt0.0058
s_similar_dist
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1710
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms44

Software

Software
Software NamePurpose
SHELXL-97refinement
SHELXphasing
HKL-2000data reduction
HKL-2000data scaling