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Alpha-amylase B in complex with maltotetraose and alpha-cyclodextrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BC9 PDB ENTRY 3BC9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 0.2M sodium acetate, 0.1M Mes-OH, 20% (w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.26 62.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.7 α = 90 b = 78.05 β = 98.9 c = 50.64 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm mirrors 2007-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.0412 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.15 30 97.9 0.057 18 3.8 47080 47080
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.2 96 0.463 3.6 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 3BC9 2.2 30 43089 43089 898 98.15 0.19685 0.19595 0.218 0.24008 0.2509 RANDOM 9.137
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] 0.19 0.38 1.16 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_4_deg 17.689 r_dihedral_angle_3_deg 16.556 r_dihedral_angle_1_deg 6.77 r_scangle_it 3.526 r_scbond_it 2.352 r_angle_refined_deg 1.939 r_angle_other_deg 1.597 r_mcangle_it 1.493 r_mcbond_it 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.667 r_dihedral_angle_4_deg 17.689 r_dihedral_angle_3_deg 16.556 r_dihedral_angle_1_deg 6.77 r_scangle_it 3.526 r_scbond_it 2.352 r_angle_refined_deg 1.939 r_angle_other_deg 1.597 r_mcangle_it 1.493 r_mcbond_it 1.013 r_metal_ion_refined 0.299 r_mcbond_other 0.228 r_nbd_refined 0.218 r_nbd_other 0.207 r_nbtor_refined 0.195 r_xyhbond_nbd_refined 0.182 r_symmetry_vdw_other 0.171 r_symmetry_hbond_refined 0.135 r_symmetry_vdw_refined 0.128 r_chiral_restr 0.115 r_nbtor_other 0.095 r_xyhbond_nbd_other 0.044 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4747 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 164
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing