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Structure of Thaumatin collected at 100K on ID30B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E0A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1 M HEPES, 0.7 M sodium/potassium tartrate and 20% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.85 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.951 α = 90 b = 57.951 β = 90 c = 150.725 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 PIXEL DECTRIS PILATUS3 6M Be CRL (vertical focusing) and Rh coating elliptical mirror (horizontal focusing) 2017-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.9787 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 1.08 54.09 89.9 0.054 0.069 0.029 0.996 11.8 3.6 99222 11.6
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 1.08 1.12 63.5 0.514 0.845 0.544 0.857 0.8 1.6
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 3e0a 1.08 54.09 91794 4831 87.37 0.149 0.14808 0.1502 0.16645 0.1671 RANDOM 17.711
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] -0.5 -0.5 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.201 r_sphericity_free 27.678 r_dihedral_angle_4_deg 17.695 r_sphericity_bonded 11.66 r_dihedral_angle_3_deg 10.88 r_dihedral_angle_1_deg 10.292 r_long_range_B_refined 3.11 r_rigid_bond_restr 3.079 r_long_range_B_other 2.898 r_scangle_other 2.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.201 r_sphericity_free 27.678 r_dihedral_angle_4_deg 17.695 r_sphericity_bonded 11.66 r_dihedral_angle_3_deg 10.88 r_dihedral_angle_1_deg 10.292 r_long_range_B_refined 3.11 r_rigid_bond_restr 3.079 r_long_range_B_other 2.898 r_scangle_other 2.735 r_scbond_other 2.287 r_scbond_it 2.279 r_mcangle_other 1.907 r_mcangle_it 1.902 r_angle_refined_deg 1.822 r_mcbond_it 1.477 r_mcbond_other 1.399 r_angle_other_deg 1.076 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_gen_planes_other 0.005 r_bond_other_d 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 1547 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction pointless data scaling PHASER phasing