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Crystal structure of TeGH116 from Thermosynechococcus elongatus with glucose
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 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 268.999 α = 90 b = 55.094 β = 131.858 c = 181.996 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 26.535 97.9 0.198 0.28 0.198 0.976 5.4 3.8 132197
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 2.03 96.4 1.031 1.458 1.031 0.434 1.3 3.9
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 26.535 132195 6491 97.863 0.17 0.1694 0.1752 0.1894 0.1947 18.459
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] -0.703 -0.546 -0.67 0.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.152 r_dihedral_angle_3_deg 13.489 r_dihedral_angle_1_deg 7.586 r_lrange_it 5.649 r_lrange_other 5.631 r_dihedral_angle_2_deg 4.829 r_scangle_it 4.613 r_scangle_other 4.613 r_scbond_it 3.035 r_scbond_other 3.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.152 r_dihedral_angle_3_deg 13.489 r_dihedral_angle_1_deg 7.586 r_lrange_it 5.649 r_lrange_other 5.631 r_dihedral_angle_2_deg 4.829 r_scangle_it 4.613 r_scangle_other 4.613 r_scbond_it 3.035 r_scbond_other 3.035 r_mcangle_other 2.979 r_mcangle_it 2.977 r_mcbond_it 2.034 r_mcbond_other 2.024 r_angle_refined_deg 1.854 r_angle_other_deg 0.663 r_nbd_other 0.217 r_nbd_refined 0.213 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.164 r_symmetry_nbd_refined 0.145 r_symmetry_xyhbond_nbd_refined 0.125 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.083 r_metal_ion_refined 0.082 r_symmetry_xyhbond_nbd_other 0.028 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12475 Nucleic Acid Atoms Solvent Atoms 617 Heterogen Atoms 100
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection autoPROC data processing MOLREP phasing