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Crystal structure of the non-heme alpha ketoglutarate dependent epimerase SnoN from nogalamycin biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OPW ensemble of 2opw, 2a1x, 2fct experimental model PDB 2A1X ensemble of 2opw, 2a1x, 2fct experimental model PDB 2FCT ensemble of 2opw, 2a1x, 2fct
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 PEG3350, ammonium acetate, Bis-Tris, ammonium ferric citrate, alpha ketoglutarate, sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.207 α = 90 b = 120.557 β = 92.54 c = 102.879 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 PIXEL DECTRIS PILATUS 6M 2015-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9724 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 2.07 47.8 99.5 0.077 11.7 4.9 379883 76968 37.7
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 2.07 2.13 99.5 0.995 1.4
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 ensemble of 2opw, 2a1x, 2fct 2.13 47.8 67031 3557 99.37 0.17725 0.17585 0.184 0.20312 0.2108 RANDOM 48.491
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] -1.1 -0.46 2.28 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.037 r_dihedral_angle_4_deg 20.839 r_dihedral_angle_3_deg 13.484 r_long_range_B_refined 7.677 r_long_range_B_other 7.63 r_dihedral_angle_1_deg 7.213 r_scangle_other 4.084 r_mcangle_other 3.211 r_mcangle_it 3.21 r_scbond_it 2.519
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.037 r_dihedral_angle_4_deg 20.839 r_dihedral_angle_3_deg 13.484 r_long_range_B_refined 7.677 r_long_range_B_other 7.63 r_dihedral_angle_1_deg 7.213 r_scangle_other 4.084 r_mcangle_other 3.211 r_mcangle_it 3.21 r_scbond_it 2.519 r_scbond_other 2.519 r_mcbond_it 2.012 r_mcbond_other 2.002 r_angle_other_deg 1.961 r_angle_refined_deg 1.959 r_chiral_restr 0.11 r_bond_refined_d 0.021 r_gen_planes_refined 0.014 r_bond_other_d 0.012 r_gen_planes_other 0.01 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 7565 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing