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The 0.95 angstrom structure of thaumatin crystallized in high-strength agarose hydrogel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 293 0.1 M Hepes-NaOH (pH 7.0), 0.33 M Na/K tartrate
Crystal Properties Matthews coefficient Solvent content 2.82 56.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.839 α = 90 b = 57.839 β = 90 c = 149.552 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 RAYONIX MX225HE 2009-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 0.95 53.95 92.9 0.054 21.5 7.5 148780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.97 56 0.35 2.25 2.3
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 2VHK 0.95 53.95 141256 7455 92.98 0.1278 0.12695 0.1301 0.14402 0.1473 RANDOM 13.695
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] 0.24 0.24 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.406 r_sphericity_free 23.081 r_dihedral_angle_4_deg 16.139 r_dihedral_angle_3_deg 11.95 r_rigid_bond_restr 7.456 r_dihedral_angle_1_deg 7.098 r_sphericity_bonded 6.854 r_long_range_B_refined 3.182 r_long_range_B_other 2.563 r_scangle_other 2.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.406 r_sphericity_free 23.081 r_dihedral_angle_4_deg 16.139 r_dihedral_angle_3_deg 11.95 r_rigid_bond_restr 7.456 r_dihedral_angle_1_deg 7.098 r_sphericity_bonded 6.854 r_long_range_B_refined 3.182 r_long_range_B_other 2.563 r_scangle_other 2.298 r_scbond_it 2.242 r_scbond_other 2.241 r_angle_refined_deg 2.221 r_mcangle_it 1.693 r_mcangle_other 1.59 r_mcbond_it 1.359 r_mcbond_other 1.359 r_angle_other_deg 1.024 r_chiral_restr 0.154 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 274 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction HKL-2000 data scaling MOLREP phasing