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Structure of a F112H variant 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 8.6 298 anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M HEPPS, 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 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.814 α = 90 b = 80.814 β = 90 c = 89.492 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 1.17 50 99.6 0.07 41.478 4.4 73398
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 1.17 1.21 97.3 0.179 2 7150
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 MOLECULAR REPLACEMENT THROUGHOUT 1.17 30 73249 3689 99.41 0.161 0.16 0.1602 0.182 0.1826 RANDOM 15.109
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] 0.11 0.05 0.11 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.162 r_dihedral_angle_4_deg 14.782 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 5.841 r_scangle_it 3.616 r_angle_refined_deg 2.849 r_scbond_it 2.651 r_mcangle_it 1.801 r_mcbond_it 1.043 r_chiral_restr 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.162 r_dihedral_angle_4_deg 14.782 r_dihedral_angle_3_deg 11.727 r_dihedral_angle_1_deg 5.841 r_scangle_it 3.616 r_angle_refined_deg 2.849 r_scbond_it 2.651 r_mcangle_it 1.801 r_mcbond_it 1.043 r_chiral_restr 0.37 r_nbtor_refined 0.323 r_symmetry_hbond_refined 0.32 r_nbd_refined 0.252 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.193 r_metal_ion_refined 0.107 r_symmetry_metal_ion_refined 0.074 r_bond_refined_d 0.022 r_gen_planes_refined 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1511 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 100
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction