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Pyridine synthase, TbtD, from thiomuracin biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5W98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 0.4 M NaH2PO4, 1 M KH2PO4 pH 6.5
Crystal Properties Matthews coefficient Solvent content 4.79 74.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.83 α = 90 b = 155.83 β = 90 c = 165.239 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 MARMOSAIC 300 mm CCD 2015-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 2.8 55.08 93.9 0.117 10 6.3 34569
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 5W98 2.8 104.52 32840 1729 93.91 0.19967 0.19748 0.1996 0.24167 0.2397 RANDOM 88.879
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.692 r_dihedral_angle_3_deg 21.011 r_dihedral_angle_4_deg 19.486 r_long_range_B_refined 14.274 r_long_range_B_other 14.273 r_mcangle_it 11.364 r_mcangle_other 11.363 r_scangle_other 11.138 r_mcbond_it 7.893 r_mcbond_other 7.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.692 r_dihedral_angle_3_deg 21.011 r_dihedral_angle_4_deg 19.486 r_long_range_B_refined 14.274 r_long_range_B_other 14.273 r_mcangle_it 11.364 r_mcangle_other 11.363 r_scangle_other 11.138 r_mcbond_it 7.893 r_mcbond_other 7.887 r_dihedral_angle_1_deg 7.809 r_scbond_it 7.713 r_scbond_other 7.712 r_angle_refined_deg 1.87 r_angle_other_deg 1.179 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4874 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing