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Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose
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, HANGING DROP 4.6 279 100 mM sodium acetate pH 4.6, 200 mM ammonium sulfate, 12.8% PEG-MME 2000.
Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.3 mM GlcMan4OMe (10 x molar ratio). 500 nl protein solution and 500 nl reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.07 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.752 α = 90 b = 81.68 β = 92.934 c = 52.994 γ = 90
Symmetry Space Group P 1 21 1
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 1.1 52.92 97.6 0.054 0.061 0.029 0.998 11.9 3.7 143298 8.98
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 1.1 1.12 71.3 0.223 0.271 0.15 0.944 3.3 2.6
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 6ZDF 1.1 52.92 143263 7225 97.529 0.107 0.1063 0.1068 0.1279 0.1284 14.999
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] -0.257 -0.173 0.472 -0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_3_deg 12.836 r_dihedral_angle_4_deg 11.791 r_rigid_bond_restr 11.682 r_dihedral_angle_1_deg 11.196 r_lrange_it 3.474 r_lrange_other 3.472 r_scangle_it 2.554 r_scangle_other 2.554 r_angle_other_deg 2.503
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.659 r_dihedral_angle_3_deg 12.836 r_dihedral_angle_4_deg 11.791 r_rigid_bond_restr 11.682 r_dihedral_angle_1_deg 11.196 r_lrange_it 3.474 r_lrange_other 3.472 r_scangle_it 2.554 r_scangle_other 2.554 r_angle_other_deg 2.503 r_mcangle_it 2.319 r_mcangle_other 2.318 r_angle_refined_deg 2.077 r_scbond_it 1.974 r_scbond_other 1.974 r_mcbond_other 1.705 r_mcbond_it 1.704 r_symmetry_nbd_refined 0.283 r_nbd_other 0.236 r_nbd_refined 0.234 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.172 r_chiral_restr 0.158 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.079 r_bond_other_d 0.033 r_bond_refined_d 0.018 r_gen_planes_other 0.018 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2922 Nucleic Acid Atoms Solvent Atoms 478 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing