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Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol cyclosulfate 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 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.583 α = 90 b = 102.94 β = 103.812 c = 75.623 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 1.5 59.78 98.7 0.999 10.3 6.8 153290
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 1.5 1.53 0.917
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 1.5 59.78 153221 7597 98.507 0.158 0.1569 0.157 0.1859 0.1859 20.58
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] 0.852 -0.956 2.794 -2.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.459 r_dihedral_angle_3_deg 13.262 r_dihedral_angle_4_deg 12.215 r_dihedral_angle_1_deg 6.897 r_lrange_it 4.182 r_lrange_other 4.072 r_scangle_it 3.443 r_scangle_other 3.443 r_angle_other_deg 2.432 r_scbond_it 2.374
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.459 r_dihedral_angle_3_deg 13.262 r_dihedral_angle_4_deg 12.215 r_dihedral_angle_1_deg 6.897 r_lrange_it 4.182 r_lrange_other 4.072 r_scangle_it 3.443 r_scangle_other 3.443 r_angle_other_deg 2.432 r_scbond_it 2.374 r_scbond_other 2.374 r_mcangle_it 2.115 r_mcangle_other 2.115 r_angle_refined_deg 1.737 r_mcbond_it 1.589 r_mcbond_other 1.584 r_nbd_refined 0.223 r_nbd_other 0.213 r_symmetry_nbd_other 0.212 r_symmetry_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.098 r_metal_ion_refined 0.075 r_symmetry_nbtor_other 0.072 r_bond_other_d 0.037 r_symmetry_nbd_refined 0.026 r_symmetry_xyhbond_nbd_other 0.023 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 7372 Nucleic Acid Atoms Solvent Atoms 785 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing