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1.8 Angstrom crystal structure of Listeria monocytogenes Lmo0184 alpha-1,6-glucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UOK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 300 Crystallization condition: JCSG+ H8 (Qiagen) 0.1 M Am Acetate, 0.1 M Bis-tris (pH 5.5), 17% Peg 10000
Protein condition: 9 mg/ml + 10 mM Tris (pH 8.3), 500 mM NaCl, 50 mM glucose
Crystal Properties Matthews coefficient Solvent content 2.26 45.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.123 α = 90 b = 103.937 β = 90 c = 193.79 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 2015-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.978 APS 21-ID-F
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 1.8 30 99.6 0.109 17.2 6.7 162894
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 1.8 1.83 100 0.741 2.6 6.4
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 1UOK 1.8 30 154761 7982 99.14 0.15525 0.15355 0.1634 0.18837 0.1959 RANDOM 22.386
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] -0.23 -0.58 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_dihedral_angle_4_deg 15.897 r_dihedral_angle_3_deg 11.875 r_dihedral_angle_1_deg 6.192 r_long_range_B_refined 5.402 r_long_range_B_other 5.402 r_angle_refined_deg 1.38 r_scangle_other 1.18 r_angle_other_deg 0.959 r_mcangle_it 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.083 r_dihedral_angle_4_deg 15.897 r_dihedral_angle_3_deg 11.875 r_dihedral_angle_1_deg 6.192 r_long_range_B_refined 5.402 r_long_range_B_other 5.402 r_angle_refined_deg 1.38 r_scangle_other 1.18 r_angle_other_deg 0.959 r_mcangle_it 0.928 r_mcangle_other 0.928 r_scbond_it 0.714 r_scbond_other 0.714 r_mcbond_it 0.54 r_mcbond_other 0.54 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13737 Nucleic Acid Atoms Solvent Atoms 1761 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing