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Crystal structure of Sweet Potato Beta-Amylase complexed with Maltotetraose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 293 0.1M Na Acetate (pH 5.5), 0.05M Tris (pH 7.5), 0.01M NaCl, 2% Isopropanol and 18% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.44 49.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.547 α = 90 b = 128.547 β = 90 c = 66.207 γ = 90
Symmetry Space Group P 42 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror 2016-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.49 90.9 98.7 0.144 6.7 4.6 19723
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 99.5 0.722 0.687 4.5
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5wqs 2.49 90.9 18743 956 98.66 0.1704 0.16648 0.1741 0.24504 0.2421 RANDOM 43.456
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] -0.04 -0.04 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.8 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_3_deg 15.28 r_long_range_B_refined 7.494 r_long_range_B_other 7.494 r_dihedral_angle_1_deg 6.356 r_scangle_other 5.805 r_mcangle_it 4.611 r_mcangle_other 4.61 r_scbond_it 3.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.8 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_3_deg 15.28 r_long_range_B_refined 7.494 r_long_range_B_other 7.494 r_dihedral_angle_1_deg 6.356 r_scangle_other 5.805 r_mcangle_it 4.611 r_mcangle_other 4.61 r_scbond_it 3.709 r_scbond_other 3.708 r_mcbond_it 3.032 r_mcbond_other 3.027 r_angle_refined_deg 1.811 r_angle_other_deg 1.033 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3914 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction HKL-2000 data reduction HKL data reduction HKL data scaling