☰ Navigation Tabs
Structure of Thaumatin collected from an in situ crystal collected on ID30B at 12.7 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 3.05 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.569 α = 90 b = 58.569 β = 90 c = 151.584 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) 2016-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9763 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 54.64 98.2 0.107 0.142 0.071 0.99 5.7 3.6 42124 15.2
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 98.4 0.931 1.37 0.712 0.39 1 3.5
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 39983 2130 97.45 0.13174 0.1299 0.1306 0.16688 0.167 RANDOM 22.094
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] -0.36 -0.36 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.148 r_sphericity_free 24.942 r_dihedral_angle_4_deg 13.545 r_dihedral_angle_3_deg 12.41 r_sphericity_bonded 12.379 r_dihedral_angle_1_deg 9.863 r_long_range_B_refined 3.345 r_long_range_B_other 3.266 r_scangle_other 2.961 r_scbond_other 2.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.148 r_sphericity_free 24.942 r_dihedral_angle_4_deg 13.545 r_dihedral_angle_3_deg 12.41 r_sphericity_bonded 12.379 r_dihedral_angle_1_deg 9.863 r_long_range_B_refined 3.345 r_long_range_B_other 3.266 r_scangle_other 2.961 r_scbond_other 2.366 r_scbond_it 2.362 r_rigid_bond_restr 2.345 r_mcangle_other 2.252 r_mcangle_it 2.226 r_mcbond_it 1.666 r_mcbond_other 1.596 r_angle_refined_deg 1.565 r_angle_other_deg 0.977 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 120 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing