☰ Navigation Tabs
Nostoc sp. 3335mg GT108 family enzyme D90A mutant complex with octyl-mannotetraose and Bis-Tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5 and 25% (w/v) PEG 3350; soaking in 0.5 mM octyl-mannotetraose
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.266 α = 90 b = 131.266 β = 90 c = 47.464 γ = 90
Symmetry Space Group P 43 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 EIGER X 16M 2020-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
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 1.58 65.63 100 0.104 0.108 0.029 1 17.2 25.6 57215
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) 1.58 1.61 99 4.416 4.588 1.241 0.518 0.5 26.2
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 1.581 65.63 57141 2796 99.934 0.184 0.183 0.1941 0.205 0.2162 33.391
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] 0.894 0.894 -1.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.279 r_dihedral_angle_3_deg 13.218 r_lrange_it 8.063 r_lrange_other 8.015 r_dihedral_angle_1_deg 7.637 r_dihedral_angle_2_deg 6.954 r_scangle_it 5.999 r_scangle_other 5.998 r_mcangle_it 4.289 r_mcangle_other 4.288
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.279 r_dihedral_angle_3_deg 13.218 r_lrange_it 8.063 r_lrange_other 8.015 r_dihedral_angle_1_deg 7.637 r_dihedral_angle_2_deg 6.954 r_scangle_it 5.999 r_scangle_other 5.998 r_mcangle_it 4.289 r_mcangle_other 4.288 r_scbond_it 3.946 r_scbond_other 3.945 r_mcbond_it 2.981 r_mcbond_other 2.974 r_angle_refined_deg 1.841 r_angle_other_deg 0.77 r_symmetry_xyhbond_nbd_refined 0.273 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.186 r_nbd_refined 0.182 r_nbtor_refined 0.175 r_symmetry_nbd_other 0.161 r_symmetry_nbd_refined 0.153 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2361 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing