2VI4

Atomic resolution (1.10 A) structure of purified thaumatin I grown in sodium DL-tartrate at 6 C.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KWNPDB ENTRY 1KWN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.1279MICROBATCH METHOD; PROTEIN AT 45 MG/ML IN 10MM SODIUM PHOSPHATE WITH 0.25M SODIUM DL-TARTRATE (PH=7.1) AND 10% (V/V) GLYCEROL; CRYSTALS GROWN AT 6 C
Crystal Properties
Matthews coefficientSolvent content
2.141.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.921α = 90
b = 57.921β = 90
c = 149.946γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2007-09-20MSINGLE WAVELENGTH
21x-ray100CCDADSC CCDM
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID15BESRFID15B
2SYNCHROTRONNSLS 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
11.12099.70.0624.28.21041652
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)
11.11.121000.632.18.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1KWN1.119.759877051961000.1260.1250.14RANDOM13.08
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]
0.050.05-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg14.158
r_dihedral_angle_3_deg11.284
r_dihedral_angle_1_deg6.976
r_scangle_it3.548
r_scbond_it2.711
r_mcangle_it2.15
r_angle_refined_deg1.569
r_mcbond_it1.482
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.254
r_dihedral_angle_4_deg14.158
r_dihedral_angle_3_deg11.284
r_dihedral_angle_1_deg6.976
r_scangle_it3.548
r_scbond_it2.711
r_mcangle_it2.15
r_angle_refined_deg1.569
r_mcbond_it1.482
r_nbtor_refined0.315
r_nbd_refined0.216
r_symmetry_vdw_refined0.207
r_xyhbond_nbd_refined0.14
r_symmetry_hbond_refined0.14
r_chiral_restr0.096
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms1545
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing