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Crystal structure of the epimerase SnoN in complex with Fe3+, alpha ketoglutarate and nogalamycin RO
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 5.5 293 PEG3350, ammonium acetate, BIS-Tris, FeCl3, alpha-ketoglutarate, nogalamycin RO
Crystal Properties Matthews coefficient Solvent content 2.59 52.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.908 α = 90 b = 119.742 β = 90 c = 159.447 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 2014-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9762 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 2.2 96 99.2 0.085 8.3 4 69960 69960 44.4
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 2.2 2.25 97 0.97 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 5EP9 2.2 95.75 66472 3423 99.03 0.20122 0.19929 0.209 0.23804 0.2455 RANDOM 60.924
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 0.92 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.083 r_dihedral_angle_4_deg 18.532 r_dihedral_angle_3_deg 14.277 r_dihedral_angle_1_deg 7.189 r_long_range_B_refined 5.702 r_long_range_B_other 5.664 r_scangle_other 1.802 r_angle_refined_deg 1.798 r_angle_other_deg 1.696 r_mcangle_it 1.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.083 r_dihedral_angle_4_deg 18.532 r_dihedral_angle_3_deg 14.277 r_dihedral_angle_1_deg 7.189 r_long_range_B_refined 5.702 r_long_range_B_other 5.664 r_scangle_other 1.802 r_angle_refined_deg 1.798 r_angle_other_deg 1.696 r_mcangle_it 1.651 r_mcangle_other 1.651 r_scbond_it 1.215 r_scbond_other 1.215 r_mcbond_it 0.999 r_mcbond_other 0.998 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_other 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.009 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 7784 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing