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Crystal structure of TeGH116 from Thermosynechococcus elongatus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BVU TxGH116
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 291 1M Potassium sodium tartrate tetrahydrate, 0.1M Bis-Tris propane pH 6.8
Crystal Properties Matthews coefficient Solvent content 2.76 55.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 266.847 α = 90 b = 55.299 β = 129.724 c = 175.918 γ = 90
Symmetry Space Group C 1 2 1
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 ADSC QUANTUM 315r 2019-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1 NSRRC BL13B1
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 2.2 26.656 96.9 0.075 0.105 0.073 0.996 9 3.7 97859
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) 2.2 2.24 98.8 0.376 0.526 0.367 0.849 2.7 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 26.656 97858 4966 96.798 0.148 0.1469 0.1597 0.1742 0.1843 22.778
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] -0.597 -0.534 -1.127 1.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.582 r_dihedral_angle_3_deg 13.752 r_dihedral_angle_1_deg 7.549 r_dihedral_angle_2_deg 6.875 r_lrange_it 5.857 r_lrange_other 5.832 r_scangle_it 4.922 r_scangle_other 4.922 r_scbond_it 3.411 r_scbond_other 3.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.582 r_dihedral_angle_3_deg 13.752 r_dihedral_angle_1_deg 7.549 r_dihedral_angle_2_deg 6.875 r_lrange_it 5.857 r_lrange_other 5.832 r_scangle_it 4.922 r_scangle_other 4.922 r_scbond_it 3.411 r_scbond_other 3.411 r_mcangle_other 3.219 r_mcangle_it 3.218 r_mcbond_it 2.326 r_mcbond_other 2.326 r_angle_refined_deg 1.843 r_angle_other_deg 0.667 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.208 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.185 r_nbd_other 0.181 r_symmetry_nbd_refined 0.167 r_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.107 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.046 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12452 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection autoPROC data processing MOLREP phasing