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Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7TAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.14 42.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.766 α = 90 b = 98.993 β = 103.6 c = 75.45 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 EIGER2 X 16M 2019-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979499 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.35 73.33 95.5 0.997 7.5 3.9 192831
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 0.76
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 7taa 1.35 73.33 192746 9485 95.314 0.179 0.1775 0.1775 0.2043 0.2041 17.351
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] -0.681 -0.297 3.193 -2.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_4_deg 11.062 r_dihedral_angle_1_deg 7.079 r_lrange_it 3.952 r_lrange_other 3.804 r_scangle_it 2.913 r_scangle_other 2.912 r_angle_other_deg 2.514 r_mcangle_other 2.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.466 r_dihedral_angle_3_deg 13.183 r_dihedral_angle_4_deg 11.062 r_dihedral_angle_1_deg 7.079 r_lrange_it 3.952 r_lrange_other 3.804 r_scangle_it 2.913 r_scangle_other 2.912 r_angle_other_deg 2.514 r_mcangle_other 2.044 r_mcangle_it 2.043 r_scbond_it 1.98 r_scbond_other 1.98 r_angle_refined_deg 1.748 r_mcbond_it 1.486 r_mcbond_other 1.471 r_nbd_refined 0.216 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.176 r_nbd_other 0.173 r_symmetry_xyhbond_nbd_refined 0.171 r_xyhbond_nbd_refined 0.145 r_metal_ion_refined 0.113 r_symmetry_nbd_refined 0.106 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.043 r_bond_other_d 0.037 r_gen_planes_other 0.018 r_bond_refined_d 0.012 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7368 Nucleic Acid Atoms Solvent Atoms 687 Heterogen Atoms 153
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing