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Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M MES, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium chloride, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.679 α = 90 b = 67.679 β = 90 c = 111.18 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 CCD SBC-3 2007-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
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 1.38 50 97.3 0.063 47.679 6.3 38038
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 1.38 1.43 82 0.097 3.1 3192
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 THROUGHOUT 1.38 50 38032 1902 97.34 0.165 0.164 0.1647 0.182 0.1822 RANDOM 14.355
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] 0.24 0.12 0.24 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_4_deg 12.925 r_dihedral_angle_3_deg 11.109 r_dihedral_angle_1_deg 5.175 r_scangle_it 3.11 r_scbond_it 2.016 r_angle_refined_deg 1.955 r_mcangle_it 1.307 r_mcbond_it 0.703 r_symmetry_hbond_refined 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.4 r_dihedral_angle_4_deg 12.925 r_dihedral_angle_3_deg 11.109 r_dihedral_angle_1_deg 5.175 r_scangle_it 3.11 r_scbond_it 2.016 r_angle_refined_deg 1.955 r_mcangle_it 1.307 r_mcbond_it 0.703 r_symmetry_hbond_refined 0.353 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.221 r_chiral_restr 0.211 r_xyhbond_nbd_refined 0.134 r_metal_ion_refined 0.076 r_symmetry_metal_ion_refined 0.056 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1462 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 99
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction