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2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 10.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM NAD;
Screen: Classics II (B11) 2.1M DL-malic acid pH 7.0;
Cryo: Screen + 20% glycerol.
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.226 α = 90 b = 85.226 β = 90 c = 228.858 γ = 120
Symmetry Space Group P 32 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 MARMOSAIC 300 mm CCD C(111) 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.25 30 100 0.102 0.102 0.109 0.037 22.9 8.5 46596 -3 40.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 100 0.782 0.782 0.832 0.282 0.854 3 8.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.25 29.89 44168 2358 99.81 0.15612 0.15427 0.1691 0.19129 0.201 RANDOM 49.003
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] 0.94 0.47 0.94 -3.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.14 r_dihedral_angle_4_deg 13.259 r_dihedral_angle_3_deg 10.27 r_long_range_B_refined 5.737 r_long_range_B_other 5.628 r_scangle_other 3.599 r_dihedral_angle_1_deg 3.272 r_mcangle_it 2.65 r_mcangle_other 2.649 r_scbond_it 2.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.14 r_dihedral_angle_4_deg 13.259 r_dihedral_angle_3_deg 10.27 r_long_range_B_refined 5.737 r_long_range_B_other 5.628 r_scangle_other 3.599 r_dihedral_angle_1_deg 3.272 r_mcangle_it 2.65 r_mcangle_other 2.649 r_scbond_it 2.34 r_scbond_other 2.339 r_mcbond_it 1.709 r_mcbond_other 1.705 r_angle_refined_deg 1.365 r_angle_other_deg 0.444 r_chiral_restr 0.068 r_gen_planes_refined 0.041 r_gen_planes_other 0.037 r_bond_refined_d 0.007 r_bond_other_d 0.001 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 6807 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing