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Crystal structure of Barley Beta-Amylase complexed with 3,4- epoxybutyl alpha-D-glucopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B1Y PDB ENTRY 1B1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 CRYSTALS WERE GROWN AT 291 K USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.5
Crystal Properties Matthews coefficient Solvent content 1.91 35.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.631 α = 90 b = 71.158 β = 90 c = 92.273 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 CCD MARMOSAIC 225 mm CCD 2007-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
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 1.16 26.13 98 0.07 6.21 6.48 109532 -9 14.2
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 1.3 1.37 86.8 0.5 1.48 3.88
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 PDB ENTRY 1B1Y 1.3 24.701 109295 5424 98.075 0.129 0.1279 0.1325 0.1578 0.1607 RANDOM 11
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] 0.304 -0.038 -0.267
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.969 r_dihedral_angle_4_deg 16.16 r_dihedral_angle_3_deg 11.948 r_sphericity_free 7.994 r_dihedral_angle_1_deg 6.63 r_scangle_it 4.305 r_sphericity_bonded 3.996 r_scbond_it 3.141 r_mcangle_it 2.127 r_rigid_bond_restr 1.808
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.969 r_dihedral_angle_4_deg 16.16 r_dihedral_angle_3_deg 11.948 r_sphericity_free 7.994 r_dihedral_angle_1_deg 6.63 r_scangle_it 4.305 r_sphericity_bonded 3.996 r_scbond_it 3.141 r_mcangle_it 2.127 r_rigid_bond_restr 1.808 r_angle_refined_deg 1.586 r_mcbond_it 1.46 r_mcbond_other 0.63 r_symmetry_vdw_other 0.182 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3888 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing