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Crystal structure of Bacillus paralicheniformis alpha-amylase in complex with beta-cyclodextrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TOY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 41 - 46 % Tacsimate, 10 mM CaCl2
Crystal Properties Matthews coefficient Solvent content 3 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.94 α = 90 b = 82.94 β = 90 c = 187.2 γ = 90
Symmetry Space Group P 43 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 110 IMAGE PLATE MARRESEARCH 2017-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 1.93 46.8 98.5 0.184 0.197 0.071 0.993 7.8 7.6 49463 9.7
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 1.93 1.97 77.1 0.804 0.871 0.328 0.609 6.7
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 FOURIER SYNTHESIS THROUGHOUT 6TOY 1.94 46.8 46912 2427 99.53 0.1723 0.1709 0.1801 0.2 0.2073 RANDOM 21.669
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] -0.18 -0.18 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.972 r_dihedral_angle_4_deg 18.621 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 5.959 r_angle_refined_deg 1.461 r_angle_other_deg 0.966 r_chiral_restr 0.087 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 34.972 r_dihedral_angle_4_deg 18.621 r_dihedral_angle_3_deg 12.502 r_dihedral_angle_1_deg 5.959 r_angle_refined_deg 1.461 r_angle_other_deg 0.966 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3910 Nucleic Acid Atoms Solvent Atoms 419 Heterogen Atoms 88
Software Software Software Name Purpose MOSFLM data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing