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Crystal structure of non-heme alpha ketoglutarate dependent carbocyclase SnoK from nogalamycin biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG MME 550, magnesium chloride, Tris/HCl, alpha ketoglutarate, ammonium ferric citrate
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.009 α = 90 b = 83.151 β = 90 c = 271.677 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 PIXEL DECTRIS PILATUS 6M 2014-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9793 ESRF ID29
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 2.24 47.7 99.4 0.133 6.2 3.7 96076 29.8
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) 1 2.24 2.32 97.9 0.632 1.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 5EP9 2.24 47.7 1 78850 4146 99.03 0.19504 0.19332 0.1994 0.22812 0.2348 RANDOM 34.704
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] -0.33 0.22 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.879 r_dihedral_angle_4_deg 14.158 r_dihedral_angle_3_deg 13.13 r_dihedral_angle_1_deg 6.646 r_long_range_B_refined 6.541 r_long_range_B_other 6.468 r_scangle_other 2.769 r_mcangle_it 1.947 r_mcangle_other 1.947 r_scbond_other 1.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.879 r_dihedral_angle_4_deg 14.158 r_dihedral_angle_3_deg 13.13 r_dihedral_angle_1_deg 6.646 r_long_range_B_refined 6.541 r_long_range_B_other 6.468 r_scangle_other 2.769 r_mcangle_it 1.947 r_mcangle_other 1.947 r_scbond_other 1.828 r_scbond_it 1.827 r_angle_refined_deg 1.502 r_angle_other_deg 1.296 r_mcbond_it 1.152 r_mcbond_other 1.152 r_chiral_restr 0.084 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.008 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 12138 Nucleic Acid Atoms Solvent Atoms 999 Heterogen Atoms 69
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing