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Structure of Bacillus halmapalus alpha-amylase, crystallized with the substrate analogue acarbose and maltose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W9X PDB ENTRY 1W9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 25 mM acarbose, 18% PEG 5K, 100 mM maltose, 6.4 mM TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.993 α = 90 b = 73.497 β = 90 c = 151.094 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 120 CCD MARMOSAIC 225 mm CCD 2005-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 1.2 MAX II I911-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 15 98.9 41708 41708
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 2 98
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 (All) 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 1W9X 1.9 14.84 39523 39523 2081 100 0.17445 0.17445 0.17236 0.1736 0.21419 0.2161 RANDOM 19.188
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] 0.6 -0.5 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.64 r_dihedral_angle_4_deg 15.439 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_1_deg 6.027 r_scangle_it 2.511 r_mcangle_it 2.358 r_scbond_it 1.708 r_angle_refined_deg 1.659 r_mcbond_it 1.446 r_nbtor_refined 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.64 r_dihedral_angle_4_deg 15.439 r_dihedral_angle_3_deg 14.365 r_dihedral_angle_1_deg 6.027 r_scangle_it 2.511 r_mcangle_it 2.358 r_scbond_it 1.708 r_angle_refined_deg 1.659 r_mcbond_it 1.446 r_nbtor_refined 0.34 r_symmetry_hbond_refined 0.321 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.206 r_symmetry_vdw_refined 0.162 r_metal_ion_refined 0.111 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3940 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data scaling MOLREP phasing