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Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6 300 ANOXIC, 13% PEG 8000, 0.1 M MES, 200 mM KCl, 33 ug/mL FMN reductase, 20 mM NADH, 2 mM FMN, 2 mM hydroxycobalamin, 3 mM MgCl2, 3 mM ATP, pH 6, vapor diffusion, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.814 α = 90 b = 67.814 β = 90 c = 111.163 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 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 1.9 30 97.4 0.093 8.2 3.5 16892 10.7
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 1.9 1.95 98.1 0.282 2.4 2.2
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 THROUGHOUT 1.9 30 14785 731 98.34 0.157 0.155 0.1549 0.204 0.2048 RANDOM 8.782
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] 0.03 0.02 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.859 r_dihedral_angle_4_deg 17.93 r_dihedral_angle_3_deg 12.289 r_dihedral_angle_1_deg 10.602 r_scangle_it 2.744 r_angle_refined_deg 2.045 r_scbond_it 1.93 r_mcangle_it 1.087 r_mcbond_it 0.667 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.859 r_dihedral_angle_4_deg 17.93 r_dihedral_angle_3_deg 12.289 r_dihedral_angle_1_deg 10.602 r_scangle_it 2.744 r_angle_refined_deg 2.045 r_scbond_it 1.93 r_mcangle_it 1.087 r_mcbond_it 0.667 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.248 r_nbd_refined 0.218 r_chiral_restr 0.202 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.147 r_metal_ion_refined 0.117 r_symmetry_metal_ion_refined 0.042 r_bond_refined_d 0.014 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1487 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 105
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing