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Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha-D-mannopyranosyl-(1-deoxynojirimycin)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 15% Polyacrylate, 100 mM Tris pH 8
Crystal Properties Matthews coefficient Solvent content 1.96 37.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.2 α = 90 b = 99.32 β = 90 c = 64.53 γ = 90
Symmetry Space Group P 21 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 PIXEL DECTRIS PILATUS 6M 2013-05-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 73.2 98 0.059 0.063 0.021 0.999 18.9 8 54088 22.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.71 99.2 1.041 1.123 0.402 0.631 7.5
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 2XFR 1.67 73.2 48428 2601 92.25 0.1636 0.1619 0.1728 0.1961 0.2046 RANDOM 33.477
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] -1.04 -1.69 2.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.546 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 13.028 r_dihedral_angle_1_deg 5.813 r_angle_refined_deg 1.425 r_angle_other_deg 0.979 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.546 r_dihedral_angle_4_deg 17.18 r_dihedral_angle_3_deg 13.028 r_dihedral_angle_1_deg 5.813 r_angle_refined_deg 1.425 r_angle_other_deg 0.979 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3867 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 23
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing