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Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with tetrasaccharide N-glycan fragment and hexatungstotellurate(VI) TEW
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 100 mM HEPES pH 7.5 - 8.1, 200 mM MgCl2, 25-27.5% v/v PEG 400, 1 mM TEW
Protein in 25 mM HEPES pH 7.0, 200 mM NaCl buffer at 10 mg/ml.
Crystal Properties Matthews coefficient Solvent content 2.71 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.414 α = 90 b = 129.414 β = 90 c = 50.201 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 2019-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95004 Diamond I04
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 1.957 112.076 50.1 0.093 0.098 0.029 0.999 15.7 11.7 17490
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 1.957 2.155 11.9 1.448 1.522 0.463 0.658 1.6 10.5
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 6ZFA 1.957 64.707 17488 844 50.122 0.187 0.1838 0.1947 0.2524 0.2625 40.367
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] -0.063 -0.032 -0.063 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_3_deg 15.956 r_dihedral_angle_4_deg 13.486 r_dihedral_angle_1_deg 7.275 r_lrange_it 7.177 r_lrange_other 7.166 r_scangle_it 5.298 r_scangle_other 5.297 r_mcangle_other 4.767 r_mcangle_it 4.758
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.769 r_dihedral_angle_3_deg 15.956 r_dihedral_angle_4_deg 13.486 r_dihedral_angle_1_deg 7.275 r_lrange_it 7.177 r_lrange_other 7.166 r_scangle_it 5.298 r_scangle_other 5.297 r_mcangle_other 4.767 r_mcangle_it 4.758 r_scbond_it 3.839 r_scbond_other 3.839 r_mcbond_it 3.259 r_mcbond_other 3.229 r_angle_refined_deg 1.76 r_angle_other_deg 1.211 r_symmetry_xyhbond_nbd_refined 0.321 r_nbd_other 0.209 r_nbd_refined 0.207 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.184 r_symmetry_nbd_refined 0.18 r_nbtor_refined 0.176 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.074 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2992 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement Aimless data scaling STARANISO data processing REFMAC phasing XDS data reduction