☰ Navigation Tabs
Crystal structure of the epimerase SnoN in complex with Ni2+, succinate 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, Bis-Tris, MgCl2, NiCl2, sodium succinate, nogalamycin RO
Crystal Properties Matthews coefficient Solvent content 2.55 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.324 α = 90 b = 117.784 β = 90 c = 160.964 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 MARMOSAIC 225 mm CCD 2015-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.85 48.8 99.9 0.091 13.5 4.5 32465 32465
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 2.85 3 100 0.824 1.9
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 2.85 48.8 30530 1628 99.17 0.20145 0.20024 0.236 0.22417 0.2582 RANDOM 87.152
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] 5.9 2.54 -8.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.461 r_dihedral_angle_4_deg 21.719 r_dihedral_angle_3_deg 15.088 r_dihedral_angle_1_deg 7.346 r_long_range_B_refined 3.592 r_long_range_B_other 3.592 r_angle_other_deg 1.972 r_angle_refined_deg 1.958 r_mcangle_it 1.396 r_mcangle_other 1.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.461 r_dihedral_angle_4_deg 21.719 r_dihedral_angle_3_deg 15.088 r_dihedral_angle_1_deg 7.346 r_long_range_B_refined 3.592 r_long_range_B_other 3.592 r_angle_other_deg 1.972 r_angle_refined_deg 1.958 r_mcangle_it 1.396 r_mcangle_other 1.395 r_scangle_other 1.291 r_scbond_it 1.29 r_scbond_other 1.29 r_mcbond_it 0.764 r_mcbond_other 0.764 r_chiral_restr 0.104 r_bond_refined_d 0.019 r_gen_planes_other 0.017 r_gen_planes_refined 0.013 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 7823 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing