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Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)inamide 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 dicyanocobinamide, 2 mM MgCl2, 2 mM ATP, pH 6, VAPOR DIFFUSION, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.826 α = 90 b = 67.826 β = 90 c = 111.26 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 2 30 98.2 0.109 5.7 2.5 13603
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) 2 99.9 0.26 1.7 1.5
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 30 12024 622 98.22 0.17188 0.16996 0.1721 0.20927 0.2089 RANDOM 8.122
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] 0.21 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 12.043 r_dihedral_angle_1_deg 10.019 r_scangle_it 2.523 r_angle_refined_deg 1.993 r_scbond_it 1.724 r_mcangle_it 0.993 r_mcbond_it 0.57 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.657 r_dihedral_angle_4_deg 17.22 r_dihedral_angle_3_deg 12.043 r_dihedral_angle_1_deg 10.019 r_scangle_it 2.523 r_angle_refined_deg 1.993 r_scbond_it 1.724 r_mcangle_it 0.993 r_mcbond_it 0.57 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.216 r_chiral_restr 0.197 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.116 r_symmetry_metal_ion_refined 0.094 r_metal_ion_refined 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1481 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 101
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