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Nostoc sp. 3335mg GT108 family enzyme D90A mutant complex with octyl-mannotetraose
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, HANGING DROP 293 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5 and 25% (w/v) PEG 3350, soaked in 5mM octyl-mannotetraose
Crystal Properties Matthews coefficient Solvent content 3.06 59.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.34 α = 90 b = 131.34 β = 90 c = 47.37 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 EIGER2 XE 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 1.74 92.87 100 0.184 0.191 0.051 0.999 10.5 26 43146
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) 1.74 1.77 99.9 4.524 4.702 1.277 0.417 0.7 25.6
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 1.74 92.87 43022 2130 99.851 0.199 0.1979 0.1978 0.229 0.2291 33.22
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] -0.967 -0.967 1.934
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.695 r_dihedral_angle_3_deg 10.769 r_lrange_it 7.792 r_dihedral_angle_1_deg 7.15 r_dihedral_angle_2_deg 5.683 r_scangle_it 5.304 r_mcangle_it 4.583 r_scbond_it 3.859 r_mcbond_it 3.242 r_angle_refined_deg 1.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.695 r_dihedral_angle_3_deg 10.769 r_lrange_it 7.792 r_dihedral_angle_1_deg 7.15 r_dihedral_angle_2_deg 5.683 r_scangle_it 5.304 r_mcangle_it 4.583 r_scbond_it 3.859 r_mcbond_it 3.242 r_angle_refined_deg 1.848 r_nbtor_refined 0.322 r_nbd_refined 0.203 r_symmetry_nbd_refined 0.196 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.117 r_symmetry_xyhbond_nbd_refined 0.096 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2357 Nucleic Acid Atoms Solvent Atoms 203 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing