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X-ray structure of the adduct formed in the reaction between thaumatin and a gold carbene compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QY5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 0.2 M sodium tartrate pH 7.2, 20 % polyethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.83 56.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.912 α = 90 b = 57.912 β = 90 c = 150.136 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 RIGAKU SATURN 944 mirrors 2015-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 57.91 93 0.123 37 20.9 27058
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 0.48 0.59 1.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QY5 1.7 54.03 25708 1323 93.09 0.17076 0.16988 0.1712 0.1874 0.1878 RANDOM 23.949
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] 0.13 0.13 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.11 r_dihedral_angle_4_deg 15.771 r_dihedral_angle_3_deg 12.596 r_long_range_B_other 7.35 r_long_range_B_refined 7.326 r_dihedral_angle_1_deg 6.416 r_scangle_other 2.862 r_mcangle_other 1.944 r_mcangle_it 1.942 r_scbond_it 1.702
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.11 r_dihedral_angle_4_deg 15.771 r_dihedral_angle_3_deg 12.596 r_long_range_B_other 7.35 r_long_range_B_refined 7.326 r_dihedral_angle_1_deg 6.416 r_scangle_other 2.862 r_mcangle_other 1.944 r_mcangle_it 1.942 r_scbond_it 1.702 r_scbond_other 1.701 r_angle_refined_deg 1.385 r_mcbond_it 1.191 r_mcbond_other 1.187 r_angle_other_deg 0.943 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1551 Nucleic Acid Atoms Solvent Atoms 313 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing