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Drosophila golgi alpha-mannosidase II (dGMII) in complex with swainsonine-configured alkyl indolizidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RQZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 100 mM succinate pH 7.0 and 6-12% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.27 45.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.911 α = 90 b = 90.908 β = 90 c = 132.596 γ = 90
Symmetry Space Group P 21 21 21
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 2023-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.47 74.98 99.9 0.037 0.037 0.998 8 1.9 39207
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.57 0.215 0.215 0.94 0.9
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 NONE 2.47 74.978 39206 1055 99.868 0.21 0.2079 0.2079 0.2977 0.2978 52.146
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] -0.299 0.213 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.038 r_dihedral_angle_6_deg 13.324 r_lrange_it 10.65 r_dihedral_angle_1_deg 8.389 r_dihedral_angle_2_deg 8.378 r_scangle_it 7.461 r_mcangle_it 7.099 r_scbond_it 4.808 r_mcbond_it 4.543 r_angle_refined_deg 2.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.038 r_dihedral_angle_6_deg 13.324 r_lrange_it 10.65 r_dihedral_angle_1_deg 8.389 r_dihedral_angle_2_deg 8.378 r_scangle_it 7.461 r_mcangle_it 7.099 r_scbond_it 4.808 r_mcbond_it 4.543 r_angle_refined_deg 2.072 r_nbtor_refined 0.278 r_symmetry_nbd_refined 0.179 r_nbd_refined 0.172 r_chiral_restr 0.157 r_xyhbond_nbd_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.133 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7970 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing