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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG, alpha-1,2-mannobiose and hexatungstotellurate(VI) TEW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZDK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 100 mM HEPES pH 7.5, 200 mM MgCl2, 30% v/v PEG 400 (Alfa Aesar), 1 mM Anderson-Evans polyoxotungstate TEW.
Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer.
Crystal Properties Matthews coefficient Solvent content 2.55 51.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.891 α = 90 b = 127.891 β = 90 c = 48.352 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 PILATUS 6M 2018-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 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 1.8 110.76 100 0.148 0.153 0.038 0.999 13.4 16.5 42149 21.59
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 1.8 1.84 100 0.939 0.969 0.237 0.782 2.9 16.6
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 6ZDK 1.8 110.757 42104 2094 99.936 0.187 0.1855 0.1979 0.2166 0.224 24.343
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] -0.893 -0.447 -0.893 2.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.832 r_dihedral_angle_1_deg 19.834 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 13.767 r_lrange_it 5.036 r_lrange_other 5.018 r_scangle_it 4.06 r_scangle_other 4.059 r_scbond_it 3.09 r_scbond_other 3.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.832 r_dihedral_angle_1_deg 19.834 r_dihedral_angle_4_deg 18.142 r_dihedral_angle_3_deg 13.767 r_lrange_it 5.036 r_lrange_other 5.018 r_scangle_it 4.06 r_scangle_other 4.059 r_scbond_it 3.09 r_scbond_other 3.09 r_angle_other_deg 2.732 r_mcangle_it 2.291 r_mcangle_other 2.291 r_angle_refined_deg 2.215 r_mcbond_it 1.519 r_mcbond_other 1.518 r_symmetry_nbd_refined 0.356 r_nbd_other 0.268 r_symmetry_nbd_other 0.204 r_nbd_refined 0.197 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.142 r_chiral_restr 0.137 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.092 r_bond_other_d 0.034 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_gen_planes_other 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2942 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing