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Pyridine synthase, PbtD, from GE2270 biosynthesis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 282 15% MPD, 8% PEG 6K, 0.1 M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.18 43.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.247 α = 90 b = 88.132 β = 109.78 c = 44.473 γ = 90
Symmetry Space Group P 1 21 1
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 2015-04-11 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 1.227 44.1 96.5 0.091 10.9 6.1 90136
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 1.23 1.25 83.9 0.827 0.368 2.2 5.7
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 SAD THROUGHOUT 1.23 44.07 85777 4320 96.41 0.16363 0.16249 0.1719 0.18617 0.1932 RANDOM 17.92
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 0.22 -0.82 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 21.399 r_dihedral_angle_3_deg 12.474 r_long_range_B_refined 6.061 r_dihedral_angle_1_deg 5.626 r_long_range_B_other 5.548 r_scangle_other 4.213 r_scbond_it 2.858 r_scbond_other 2.857 r_mcangle_it 2.416
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.806 r_dihedral_angle_4_deg 21.399 r_dihedral_angle_3_deg 12.474 r_long_range_B_refined 6.061 r_dihedral_angle_1_deg 5.626 r_long_range_B_other 5.548 r_scangle_other 4.213 r_scbond_it 2.858 r_scbond_other 2.857 r_mcangle_it 2.416 r_mcangle_other 2.416 r_angle_refined_deg 2.264 r_mcbond_it 1.643 r_mcbond_other 1.643 r_angle_other_deg 1.141 r_chiral_restr 0.26 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 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 2372 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AutoSol phasing