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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with HEPES and hexatungstotellurate(VI) TEW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZDF
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 2.61 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.968 α = 90 b = 128.968 β = 90 c = 48.791 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 2018-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 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 2 64.48 99.6 0.126 0.149 0.078 0.992 6.2 3.5 31607
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 2 2.05 98.3 0.739 0.869 0.45 0.411 1.5 3.5
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 6ZDF 2 64.48 31481 1554 99.592 0.198 0.1956 0.2076 0.235 0.248 32.842
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] -1.779 -0.89 -1.779 5.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.789 r_dihedral_angle_4_deg 18.755 r_dihedral_angle_3_deg 15.88 r_dihedral_angle_1_deg 6.13 r_lrange_it 5.317 r_lrange_other 5.29 r_scangle_it 4.459 r_scangle_other 3.617 r_scbond_it 3.245 r_mcangle_other 2.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.789 r_dihedral_angle_4_deg 18.755 r_dihedral_angle_3_deg 15.88 r_dihedral_angle_1_deg 6.13 r_lrange_it 5.317 r_lrange_other 5.29 r_scangle_it 4.459 r_scangle_other 3.617 r_scbond_it 3.245 r_mcangle_other 2.798 r_mcangle_it 2.793 r_angle_other_deg 2.318 r_scbond_other 2.224 r_angle_refined_deg 1.963 r_mcbond_it 1.804 r_mcbond_other 1.775 r_nbd_other 0.266 r_symmetry_nbd_refined 0.232 r_symmetry_nbd_other 0.196 r_nbd_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.129 r_symmetry_nbtor_other 0.077 r_bond_other_d 0.035 r_metal_ion_refined 0.035 r_symmetry_xyhbond_nbd_other 0.033 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2986 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing