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Thaumatin from Thaumatococcus Danielli in complex with tris-dipicolinate Europium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.7 M Sodium Potassium Tatrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.55 α = 90 b = 57.55 β = 90 c = 149.4 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm Si(111) 2004-12-25 M MAD 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 1.776211, 0.920134 ESRF BM30A 2 ESRF BM30A
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.456 45.596 99.5 0.074 0.074 5.5 12.3 44812 11.4
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) Redundancy Number Unique Reflections (All) 1 1.46 1.53 96.7 0.39 0.39 1.1 7.7 6218
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1RQW 1.46 53.68 44636 2259 99.31 0.153 0.152 0.176 0.1935 RANDOM 10.078
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] 0.06 0.06 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.729 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 12.83 r_dihedral_angle_1_deg 6.686 r_sphericity_free 4.884 r_angle_other_deg 3.975 r_scangle_it 3.064 r_scbond_it 2.192 r_mcangle_it 1.642 r_sphericity_bonded 1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.729 r_dihedral_angle_4_deg 17.205 r_dihedral_angle_3_deg 12.83 r_dihedral_angle_1_deg 6.686 r_sphericity_free 4.884 r_angle_other_deg 3.975 r_scangle_it 3.064 r_scbond_it 2.192 r_mcangle_it 1.642 r_sphericity_bonded 1.439 r_angle_refined_deg 1.416 r_rigid_bond_restr 1.212 r_mcbond_it 1.11 r_mcbond_other 0.672 r_symmetry_vdw_other 0.28 r_symmetry_vdw_refined 0.231 r_nbd_other 0.23 r_nbd_refined 0.206 r_nbtor_refined 0.186 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.156 r_nbtor_other 0.118 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_other 0.009 r_gen_planes_refined 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1551 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 57
Software Software Software Name Purpose SCALA data scaling SHARP phasing SOLOMON phasing REFMAC refinement PDB_EXTRACT data extraction BM30A data collection XDS data reduction