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Nostoc sp. 3335mg GT108 family enzyme complex with mannose-1-phosphate (M1P)
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 6.9 and 31% (w/v) PEG 3350; soaking with 5 mM Man1P
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.851 α = 90 b = 131.851 β = 90 c = 47.25 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 2020-09-26 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 1.41 93.23 99.8 0.147 0.153 0.043 0.999 7.9 24.4 80581
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) 1.41 1.43 96.9 9.571 10.111 3.24 0.638 0.1 18.4
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 1.41 93.23 80496 4058 99.923 0.205 0.2039 0.2096 0.2297 0.2352 30.683
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] 1.273 1.273 -2.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.867 r_dihedral_angle_3_deg 12.922 r_dihedral_angle_2_deg 11.567 r_dihedral_angle_1_deg 7.383 r_lrange_it 7.103 r_lrange_other 7.01 r_scangle_it 5.549 r_scangle_other 5.547 r_mcangle_it 4.235 r_mcangle_other 4.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.867 r_dihedral_angle_3_deg 12.922 r_dihedral_angle_2_deg 11.567 r_dihedral_angle_1_deg 7.383 r_lrange_it 7.103 r_lrange_other 7.01 r_scangle_it 5.549 r_scangle_other 5.547 r_mcangle_it 4.235 r_mcangle_other 4.234 r_scbond_it 3.838 r_scbond_other 3.837 r_mcbond_it 3.043 r_mcbond_other 3.043 r_angle_refined_deg 1.897 r_angle_other_deg 0.671 r_symmetry_xyhbond_nbd_refined 0.33 r_symmetry_nbd_refined 0.281 r_nbd_other 0.233 r_nbd_refined 0.218 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.185 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.098 r_symmetry_nbtor_other 0.09 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 2384 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling MOLREP phasing