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1.5 Angstrom Resolution Crystal Structure of NAD-Dependent Epimerase from Klebsiella pneumoniae in Complex with NAD.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 Protein: 7.6 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3);
Screen: PEGs II (E10), 0.2M Ammonium sulfate, 20% (w/v) PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.239 α = 90 b = 55.845 β = 93.21 c = 97.318 γ = 90
Symmetry Space Group P 1 21 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 225 mm CCD C(111) 2015-04-27 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) 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 1.5 30 99.9 0.071 0.071 24.8 4.3 102114 -3 20.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 100 0.629 0.8 2.3 4.2
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 1.5 29.21 97040 5033 99.42 0.18189 0.1804 0.1806 0.2114 0.2119 RANDOM 27.325
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] 0.27 0.49 0.78 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.568 r_dihedral_angle_4_deg 11.29 r_dihedral_angle_3_deg 10.041 r_long_range_B_refined 5.744 r_long_range_B_other 5.651 r_scangle_other 3.827 r_dihedral_angle_1_deg 3.817 r_mcangle_it 3.027 r_mcangle_other 3.027 r_scbond_it 2.509
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.568 r_dihedral_angle_4_deg 11.29 r_dihedral_angle_3_deg 10.041 r_long_range_B_refined 5.744 r_long_range_B_other 5.651 r_scangle_other 3.827 r_dihedral_angle_1_deg 3.817 r_mcangle_it 3.027 r_mcangle_other 3.027 r_scbond_it 2.509 r_scbond_other 2.509 r_mcbond_it 1.991 r_mcbond_other 1.979 r_angle_refined_deg 1.444 r_angle_other_deg 0.873 r_chiral_restr 0.086 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.01 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 4953 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing