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Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine 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 2.27 45.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.684 α = 90 b = 103.32 β = 103.827 c = 75.508 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 2019-03-07 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 1.67 103.32 100 0.997 9.6 4.2 113249
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 1.67 1.7 0.715
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 1.67 73.427 113215 5597 99.93 0.173 0.1719 0.1719 0.201 0.201 26.078
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] -0.517 -1.014 4.26 -2.893
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.591 r_dihedral_angle_3_deg 14.219 r_dihedral_angle_4_deg 11.199 r_dihedral_angle_1_deg 6.921 r_lrange_it 4.366 r_lrange_other 4.334 r_scangle_it 3.678 r_scangle_other 3.678 r_scbond_it 2.561 r_scbond_other 2.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.591 r_dihedral_angle_3_deg 14.219 r_dihedral_angle_4_deg 11.199 r_dihedral_angle_1_deg 6.921 r_lrange_it 4.366 r_lrange_other 4.334 r_scangle_it 3.678 r_scangle_other 3.678 r_scbond_it 2.561 r_scbond_other 2.561 r_mcangle_it 2.522 r_mcangle_other 2.522 r_angle_other_deg 2.45 r_mcbond_it 1.941 r_mcbond_other 1.938 r_angle_refined_deg 1.667 r_symmetry_nbd_other 0.212 r_nbd_refined 0.209 r_nbtor_refined 0.171 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.139 r_symmetry_nbd_refined 0.101 r_chiral_restr 0.087 r_metal_ion_refined 0.085 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_refined 0.067 r_bond_other_d 0.037 r_symmetry_xyhbond_nbd_other 0.019 r_gen_planes_other 0.014 r_bond_refined_d 0.01 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7368 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing