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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 5.6 293 : 0.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol
Crystal Properties Matthews coefficient Solvent content 2.24 45.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.214 α = 90 b = 103.1 β = 103.632 c = 75.374 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 2018-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
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 1.55 103.1 99.9 0.995 11.8 4 139975
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 1.55 1.58 0.874
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 1.55 73.358 139928 6862 99.86 0.148 0.1463 0.1464 0.1736 0.1736 16.912
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] -0.071 -0.366 1.913 -1.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_1_deg 13.393 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_4_deg 10.921 r_lrange_it 4.186 r_lrange_other 4.063 r_scangle_it 3.418 r_scangle_other 3.418 r_angle_other_deg 2.535 r_scbond_it 2.351
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_1_deg 13.393 r_dihedral_angle_3_deg 13.018 r_dihedral_angle_4_deg 10.921 r_lrange_it 4.186 r_lrange_other 4.063 r_scangle_it 3.418 r_scangle_other 3.418 r_angle_other_deg 2.535 r_scbond_it 2.351 r_scbond_other 2.351 r_mcangle_it 2.031 r_mcangle_other 2.031 r_angle_refined_deg 1.821 r_mcbond_it 1.448 r_mcbond_other 1.446 r_nbd_refined 0.231 r_symmetry_nbd_other 0.212 r_nbd_other 0.181 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.105 r_symmetry_nbtor_other 0.079 r_symmetry_nbd_refined 0.064 r_metal_ion_refined 0.059 r_bond_other_d 0.037 r_gen_planes_other 0.022 r_bond_refined_d 0.013 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7368 Nucleic Acid Atoms Solvent Atoms 815 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing