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Crystal structure of GH47 alpha-1,2-mannosidase from Caulobacter K31 strain in complex with cyclosulfamidate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AYO 4AYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 23% PEG3350, 0.1 M MES pH 7.0, 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.134 α = 90 b = 144.134 β = 90 c = 50.32 γ = 120
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 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.799 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 0.97 72.07 100 0.155 0.05 0.999 7.7 10.2 230864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.97 0.99 100 1.49 0.49 0.605 1.3 10
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4AYO 0.97 72.067 230864 11679 99.987 0.138 0.1373 0.1363 0.148 0.1467 7.642
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] -0.041 -0.021 -0.041 0.133
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.543 r_dihedral_angle_4_deg 16.508 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 6.493 r_lrange_it 3.284 r_lrange_other 2.643 r_angle_refined_deg 1.919 r_scangle_it 1.759 r_scangle_other 1.758 r_angle_other_deg 1.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.543 r_dihedral_angle_4_deg 16.508 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 6.493 r_lrange_it 3.284 r_lrange_other 2.643 r_angle_refined_deg 1.919 r_scangle_it 1.759 r_scangle_other 1.758 r_angle_other_deg 1.698 r_scbond_it 1.238 r_scbond_other 1.237 r_mcangle_other 1.04 r_mcangle_it 1.038 r_mcbond_it 0.704 r_mcbond_other 0.698 r_nbd_refined 0.233 r_nbd_other 0.227 r_symmetry_nbd_refined 0.226 r_nbtor_refined 0.19 r_symmetry_xyhbond_nbd_refined 0.182 r_symmetry_nbd_other 0.176 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.074 r_chiral_restr_other 0.052 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3446 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling