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ATP bound at the active site of a PduO type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NOG PDB ENTRY 1NOG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH 8.5 293 0.85 M Ammonium sulfate, 50 mM magnesium chloride, 150 mM sodium chloride, 1.5 mM ATP, 4 mM hydroxocobalamin, pH 8.5, BATCH, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.609 α = 90 b = 110.609 β = 90 c = 110.609 γ = 90
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 SBC-3 2005-11-21 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 1.68 50 99.4 0.046 11.3 9.5 25595
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.74 99.4 0.234 0.234 4.1 6.8 2522
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 1NOG 1.68 30 25595 1305 99.46 0.175 0.173 0.1725 0.204 0.2026 RANDOM 23.946
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.427 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_3_deg 12.146 r_dihedral_angle_1_deg 5.209 r_scangle_it 3.699 r_scbond_it 2.654 r_mcangle_it 1.687 r_angle_refined_deg 1.341 r_mcbond_it 1.056 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.427 r_dihedral_angle_4_deg 14.683 r_dihedral_angle_3_deg 12.146 r_dihedral_angle_1_deg 5.209 r_scangle_it 3.699 r_scbond_it 2.654 r_mcangle_it 1.687 r_angle_refined_deg 1.341 r_mcbond_it 1.056 r_nbtor_refined 0.304 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1440 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 49
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling