3V7V

Thaumatin by Classical Hanging Drop Vapour Diffusion after 1.81 MGy X-Ray dose at ESRF ID29 beamline (Best Case)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ALDPDB ENTRY 3ALD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52936 uL protein solution containing 18 mg/mL thaumatin in 100 mM ADA disodium salt buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.865α = 90
b = 57.865β = 90
c = 150.2γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97633ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.553.99797.80.04840.114.51201511842
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5896.40.1180.1186.315

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 3ALD2.353.9971127556398.530.184490.181480.24632RANDOM7.931
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]
0.130.13-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.617
r_dihedral_angle_4_deg16.65
r_dihedral_angle_3_deg12.896
r_dihedral_angle_1_deg6.901
r_scangle_it4.835
r_scbond_it2.961
r_angle_refined_deg1.821
r_mcangle_it1.658
r_mcbond_it0.878
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.617
r_dihedral_angle_4_deg16.65
r_dihedral_angle_3_deg12.896
r_dihedral_angle_1_deg6.901
r_scangle_it4.835
r_scbond_it2.961
r_angle_refined_deg1.821
r_mcangle_it1.658
r_mcbond_it0.878
r_chiral_restr0.116
r_bond_refined_d0.022
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_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 Atoms190
Heterogen Atoms24

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
PXSOFTdata collection
XSCALEdata scaling