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Crystal Structure of Anoxybacillus Alpha-amylase Provides Insights into a New Glycosyl Hydrolase Subclass
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 THE TASKA-MALTODP3 NAMELY TASKA-T COMPLEXES WAS CRYSTALLIZED USING THE STREAK SEEDING METHOD WITH A COMMERCIALLY AVAILABLE SEEDING TOOL, HAMPTON RESEARCH, USA. THE SEEDING TOOL WAS DIPPED INTO A DROP CONTAINING TASKA-APO,PDB ID 5A2A, CRYSTALS AND STREAKED ON THE DROPS THAT CONSISTED OF 0.3 UL 6 MG/ML TASKA PROTEIN AND 0.3 UL RESERVOIR SOLUTION 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, AND 18 % W/V POLYETHYLENE GLYCOL 8,000 WITH 20 MM MALTOTRIOSE.
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.816 α = 90 b = 63.532 β = 90 c = 122.97 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU R-AXIS IV 2014-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.9 19.54 96.7 0.09 12.6 3.6 37601 1.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 86.6 0.58 1.9 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4E2O 1.9 61.49 35690 1861 96.39 0.1585 0.15585 0.20914 0.1857 RANDOM 21.102
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] -0.54 -0.63 1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_3_deg 14.061 r_dihedral_angle_1_deg 6.138 r_scbond_it 1.991 r_mcangle_it 1.875 r_angle_refined_deg 1.821 r_mcbond_it 1.292 r_mcbond_other 1.284 r_angle_other_deg 0.884
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.821 r_dihedral_angle_4_deg 15.418 r_dihedral_angle_3_deg 14.061 r_dihedral_angle_1_deg 6.138 r_scbond_it 1.991 r_mcangle_it 1.875 r_angle_refined_deg 1.821 r_mcbond_it 1.292 r_mcbond_other 1.284 r_angle_other_deg 0.884 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3756 Nucleic Acid Atoms Solvent Atoms 518 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing