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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcIFG 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 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.864 α = 90 b = 127.864 β = 90 c = 48.809 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 0.97625 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 1.9 31.97 100 0.203 0.209 0.05 0.998 10.5 17.6 36208 30.3
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 1.9 1.94 99.8 3.43 3.534 0.843 0.546 1 17.4
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 1.9 31.97 36184 1779 99.89 0.194 0.1927 0.2062 0.2234 0.2322 29.729
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] -1.009 -0.505 -1.009 3.273
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 16.361 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_1_deg 6.008 r_lrange_it 4.321 r_lrange_other 4.299 r_scangle_it 4.283 r_scangle_other 4.283 r_scbond_it 3.238 r_scbond_other 3.238
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.506 r_dihedral_angle_4_deg 16.361 r_dihedral_angle_3_deg 14.233 r_dihedral_angle_1_deg 6.008 r_lrange_it 4.321 r_lrange_other 4.299 r_scangle_it 4.283 r_scangle_other 4.283 r_scbond_it 3.238 r_scbond_other 3.238 r_angle_other_deg 2.455 r_mcangle_it 2.273 r_mcangle_other 2.273 r_angle_refined_deg 2.073 r_mcbond_it 1.477 r_mcbond_other 1.476 r_symmetry_nbd_refined 0.348 r_nbd_other 0.278 r_nbd_refined 0.198 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.178 r_chiral_restr 0.133 r_xyhbond_nbd_refined 0.128 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.08 r_bond_other_d 0.035 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2938 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling REFMAC phasing