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Structure of a D35N variant PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 300 ANOXIC, 16% PEG 8000, 0.1 M MES, 200 mM KCl, 30 ug/mL FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydroxycobalamin, 10 mM MgCl2, 10 mM ATP, pH 6.0, vapor diffusion, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.772 α = 90 b = 64.772 β = 90 c = 169.438 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 100 CCD Bruker Platinum 135 Montel 2007-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.61 30 99.6 6.8 26.1 7.5 12422 29.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.61 2.66 99.5 0.177 4.9
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 2.61 30 11938 579 96.18 0.177 0.173 0.2184 0.249 0.2137 RANDOM 30.817
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] 0.54 0.27 0.54 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 19.178 r_dihedral_angle_3_deg 15.679 r_dihedral_angle_1_deg 5.703 r_scangle_it 2.114 r_scbond_it 1.499 r_angle_refined_deg 1.395 r_mcangle_it 0.859 r_mcbond_it 0.593 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 19.178 r_dihedral_angle_3_deg 15.679 r_dihedral_angle_1_deg 5.703 r_scangle_it 2.114 r_scbond_it 1.499 r_angle_refined_deg 1.395 r_mcangle_it 0.859 r_mcbond_it 0.593 r_nbtor_refined 0.303 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.197 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.094 r_symmetry_metal_ion_refined 0.091 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2781 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction