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Nostoc sp. 3335mg GT108 family enzyme native
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1 M Bis-Tris pH 6.5 and 28% (w/v) PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 3.01 59.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.65 α = 90 b = 130.65 β = 90 c = 47.3 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 PILATUS 6M 2020-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.0 Diamond I24
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 1.45 65.32 100 0.079 0.082 0.023 0.999 20 25.1 72944
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) 1.45 1.47 99.9 2.051 2.132 0.582 0.656 1.7 25.9
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 1.45 65.32 72875 3592 99.995 0.169 0.1685 0.1685 0.1864 0.1865 27.475
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] 0.163 0.163 -0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.204 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 9.366 r_dihedral_angle_1_deg 7.188 r_lrange_it 6.674 r_lrange_other 6.594 r_scangle_it 4.888 r_scangle_other 4.886 r_mcangle_it 3.43 r_mcangle_other 3.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.204 r_dihedral_angle_3_deg 11.31 r_dihedral_angle_2_deg 9.366 r_dihedral_angle_1_deg 7.188 r_lrange_it 6.674 r_lrange_other 6.594 r_scangle_it 4.888 r_scangle_other 4.886 r_mcangle_it 3.43 r_mcangle_other 3.429 r_scbond_it 3.384 r_scbond_other 3.383 r_mcbond_other 2.407 r_mcbond_it 2.405 r_angle_refined_deg 1.91 r_angle_other_deg 0.664 r_nbd_refined 0.207 r_nbd_other 0.201 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.159 r_symmetry_nbd_refined 0.126 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2365 Nucleic Acid Atoms Solvent Atoms 340 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement Aimless data scaling DIALS data reduction MOLREP phasing