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2.25 Angstrom Resolution Crystal Structure of 6-phospho-alpha-glucosidase from Klebsiella pneumoniae in Complex with NAD and Mn2+.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 292 Protein: 7.3 mg/ml, 0.01M Tris-HCl pH 8.3, 2mM Mn;
Screen: Classics II (G4), 0.2M Lithium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350;
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.027 α = 90 b = 86.027 β = 90 c = 230.777 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 99.7 0.092 0.092 0.099 0.036 25.2 7.4 47795 -3 46.1
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 99.5 0.833 0.833 0.894 0.324 0.837 2.5 7.5
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 28.99 45255 2527 99.69 0.16709 0.16428 0.1765 0.21896 0.2256 RANDOM 59.294
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] 1.63 0.81 1.63 -5.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.631 r_dihedral_angle_4_deg 13.733 r_dihedral_angle_3_deg 9.957 r_long_range_B_refined 7.12 r_long_range_B_other 7.098 r_scangle_other 4.701 r_mcangle_it 3.633 r_mcangle_other 3.633 r_dihedral_angle_1_deg 3.226 r_scbond_it 3.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.631 r_dihedral_angle_4_deg 13.733 r_dihedral_angle_3_deg 9.957 r_long_range_B_refined 7.12 r_long_range_B_other 7.098 r_scangle_other 4.701 r_mcangle_it 3.633 r_mcangle_other 3.633 r_dihedral_angle_1_deg 3.226 r_scbond_it 3.142 r_scbond_other 3.138 r_mcbond_it 2.437 r_mcbond_other 2.434 r_angle_refined_deg 1.392 r_angle_other_deg 0.449 r_chiral_restr 0.068 r_gen_planes_refined 0.04 r_gen_planes_other 0.037 r_bond_refined_d 0.008 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 6816 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing