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Structure of Thaumatin collected from an in situ crystal on ID30B at 17.5 keV.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A47
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M HEPES and 0.7 M potassium/sodium tartrate
Crystal Properties Matthews coefficient Solvent content 2.93 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.57 α = 90 b = 58.57 β = 90 c = 151.544 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 293 PIXEL DECTRIS PILATUS3 6M Be CRL (vertical focusing) and Rh stripe Elliptical mirror (horizontal focusing) 2016-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.7085 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 54.63 92.6 0.086 0.111 0.057 0.99 7.2 3.4 39794 12.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 96.7 0.727 0.979 0.518 0.6 1.3 3.4
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 5a47 1.5 54.63 37747 1985 92.02 0.1382 0.13673 0.1354 0.16678 0.1677 RANDOM 19.775
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.349 r_sphericity_free 22.123 r_dihedral_angle_4_deg 15.25 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 9.826 r_sphericity_bonded 8.756 r_long_range_B_refined 2.286 r_long_range_B_other 2.284 r_rigid_bond_restr 1.975 r_scangle_other 1.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.349 r_sphericity_free 22.123 r_dihedral_angle_4_deg 15.25 r_dihedral_angle_3_deg 11.987 r_dihedral_angle_1_deg 9.826 r_sphericity_bonded 8.756 r_long_range_B_refined 2.286 r_long_range_B_other 2.284 r_rigid_bond_restr 1.975 r_scangle_other 1.972 r_mcangle_other 1.552 r_mcangle_it 1.54 r_scbond_other 1.529 r_scbond_it 1.526 r_angle_refined_deg 1.434 r_mcbond_it 1.143 r_mcbond_other 1.085 r_angle_other_deg 0.924 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1545 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 10
Software Software Software Name Purpose MxCuBE data collection REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing