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Pyridine synthase, PbtD, from GE2270 biosynthesis bound to TSP
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 8.5 282 1.9 M lithium sulfate, 2% PEG 400, and 0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.25 α = 90 b = 66.457 β = 90 c = 116.572 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2016-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.589 41.37 99.5 0.132 14 12 46922
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.6 95.5 1.203 0.545 2 10.3
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 1.59 58.29 44486 2365 99.35 0.16377 0.16189 0.1749 0.19874 0.2124 RANDOM 16.5
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] -0.38 0.52 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.957 r_dihedral_angle_4_deg 20.933 r_dihedral_angle_3_deg 12.892 r_long_range_B_refined 5.978 r_long_range_B_other 5.502 r_dihedral_angle_1_deg 5.412 r_scangle_other 4.188 r_scbond_it 2.784 r_scbond_other 2.78 r_angle_refined_deg 1.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.957 r_dihedral_angle_4_deg 20.933 r_dihedral_angle_3_deg 12.892 r_long_range_B_refined 5.978 r_long_range_B_other 5.502 r_dihedral_angle_1_deg 5.412 r_scangle_other 4.188 r_scbond_it 2.784 r_scbond_other 2.78 r_angle_refined_deg 1.818 r_mcangle_other 1.699 r_mcangle_it 1.698 r_mcbond_it 1.212 r_mcbond_other 1.199 r_angle_other_deg 1.077 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 2531 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing