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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with bis-tris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 100 mM bis-tris pH 5.5, 25% w/v PEG 3350.
Protein at 10 mg/ml in 25 mM HEPES pH 7.0, 200 mM NaCl buffer with 2.23 mM GlcIFG and 2.23 mM alpha-1,2-mannobiose (10 x molar ratio). 300 nl droplet (150 nl protein solution, 150 nl reservoir solution). The ligand additives are probably not required for crystallization.
Crystal Properties Matthews coefficient Solvent content 2.11 41.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.812 α = 90 b = 106.994 β = 110.315 c = 43.884 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 2018-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97718 Diamond I24
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 1.2 38.41 99.4 0.049 0.057 0.028 0.999 10.6 3.8 114498 12.49
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 1.2 1.22 94.7 0.695 0.854 0.485 0.804 1.5 2.8
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 6ZFN 1.2 38.41 114455 5555 99.308 0.143 0.1409 0.144 0.1812 0.1909 23.781
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] -3.612 1.62 -0.784 2.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.039 r_rigid_bond_restr 16.007 r_dihedral_angle_4_deg 14.289 r_dihedral_angle_3_deg 12.655 r_dihedral_angle_1_deg 6.338 r_lrange_it 5.054 r_lrange_other 4.832 r_scangle_it 4.778 r_scangle_other 4.777 r_scbond_it 4.048
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.039 r_rigid_bond_restr 16.007 r_dihedral_angle_4_deg 14.289 r_dihedral_angle_3_deg 12.655 r_dihedral_angle_1_deg 6.338 r_lrange_it 5.054 r_lrange_other 4.832 r_scangle_it 4.778 r_scangle_other 4.777 r_scbond_it 4.048 r_scbond_other 4.047 r_mcangle_other 3.811 r_mcangle_it 3.759 r_mcbond_it 3.271 r_mcbond_other 3.233 r_angle_other_deg 2.353 r_angle_refined_deg 1.82 r_symmetry_xyhbond_nbd_other 0.242 r_nbd_other 0.22 r_nbd_refined 0.218 r_symmetry_nbd_other 0.212 r_symmetry_nbd_refined 0.198 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.134 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.089 r_bond_other_d 0.034 r_gen_planes_other 0.025 r_gen_planes_refined 0.014 r_bond_refined_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2865 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing