2PE7 | pdb_00002pe7

Thaumatin from Thaumatococcus Danielli in complex with tris-dipicolinate Europium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RQW 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.7 M Sodium Potassium Tatrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.55α = 90
b = 57.55β = 90
c = 149.4γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSi(111)2004-12-25MMAD
21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A1.776211, 0.920134ESRFBM30A
2ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.45645.59699.50.0740.0745.512.34481211.4
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)
11.461.5396.70.390.391.17.76218

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT1RQW1.4653.6844636225999.310.1530.1520.160.1760.18RANDOM10.078
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]
0.060.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.729
r_dihedral_angle_4_deg17.205
r_dihedral_angle_3_deg12.83
r_dihedral_angle_1_deg6.686
r_sphericity_free4.884
r_angle_other_deg3.975
r_scangle_it3.064
r_scbond_it2.192
r_mcangle_it1.642
r_sphericity_bonded1.439
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.729
r_dihedral_angle_4_deg17.205
r_dihedral_angle_3_deg12.83
r_dihedral_angle_1_deg6.686
r_sphericity_free4.884
r_angle_other_deg3.975
r_scangle_it3.064
r_scbond_it2.192
r_mcangle_it1.642
r_sphericity_bonded1.439
r_angle_refined_deg1.416
r_rigid_bond_restr1.212
r_mcbond_it1.11
r_mcbond_other0.672
r_symmetry_vdw_other0.28
r_symmetry_vdw_refined0.231
r_nbd_other0.23
r_nbd_refined0.206
r_nbtor_refined0.186
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.156
r_nbtor_other0.118
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_other0.009
r_gen_planes_refined0.006
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1551
Nucleic Acid Atoms
Solvent Atoms351
Heterogen Atoms57

Software

Software
Software NamePurpose
SCALAdata scaling
SHARPphasing
SOLOMONphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BM30Adata collection
XDSdata reduction