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Structure of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with GlcDMJ 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 2.57 52.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.549 α = 90 b = 128.549 β = 90 c = 48.264 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 2019-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 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 2.269 111.327 51.9 0.276 0.295 0.103 0.989 5.3 8 11089
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 2.269 2.536 15.4 1.52 1.617 0.547 0.569 8.6
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 6ZFA 2.269 111.327 11089 545 51.903 0.192 0.1882 0.1972 0.2559 0.2593 29.85
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] 0.579 0.289 0.579 -1.878
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_3_deg 17.512 r_dihedral_angle_4_deg 14.734 r_dihedral_angle_1_deg 7.606 r_lrange_it 6.663 r_lrange_other 6.656 r_scangle_it 3.176 r_scangle_other 3.175 r_mcangle_it 2.928 r_mcangle_other 2.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.659 r_dihedral_angle_3_deg 17.512 r_dihedral_angle_4_deg 14.734 r_dihedral_angle_1_deg 7.606 r_lrange_it 6.663 r_lrange_other 6.656 r_scangle_it 3.176 r_scangle_other 3.175 r_mcangle_it 2.928 r_mcangle_other 2.928 r_scbond_it 2.474 r_scbond_other 2.474 r_mcbond_it 1.774 r_mcbond_other 1.768 r_angle_refined_deg 1.531 r_angle_other_deg 1.126 r_symmetry_xyhbond_nbd_refined 0.338 r_symmetry_nbd_refined 0.262 r_nbd_other 0.254 r_nbd_refined 0.207 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.174 r_symmetry_nbtor_other 0.076 r_symmetry_xyhbond_nbd_other 0.06 r_chiral_restr 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2993 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling REFMAC phasing