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x-ray structure of NeoB from Streptomyces fradiae in complex with neamine as an external aldimine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 16-21% PEG-3350, 300 mM KCl, 100 mM HEPES, 5 mM neamine, 1 mM PLP
Crystal Properties Matthews coefficient Solvent content 2.22 44.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.363 α = 90 b = 107.363 β = 98.24 c = 217.528 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 ADSC QUANTUM 210r 2017-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9498 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 50 87.2 0.049 0.049 38.4 3.9 367186
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 70 0.1 0.1 7.9 2.6
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 6cbk 1.6 30 348837 18346 87.33 0.19856 0.19622 0.209 0.24283 0.2532 RANDOM 23.734
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] -1.68 -0.06 3.07 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.218 r_dihedral_angle_4_deg 17.668 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_1_deg 6.535 r_long_range_B_refined 5.685 r_long_range_B_other 5.587 r_scangle_other 4.71 r_scbond_it 3.415 r_scbond_other 3.414 r_mcangle_it 3.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.218 r_dihedral_angle_4_deg 17.668 r_dihedral_angle_3_deg 15.102 r_dihedral_angle_1_deg 6.535 r_long_range_B_refined 5.685 r_long_range_B_other 5.587 r_scangle_other 4.71 r_scbond_it 3.415 r_scbond_other 3.414 r_mcangle_it 3.212 r_mcangle_other 3.212 r_mcbond_it 2.588 r_mcbond_other 2.588 r_angle_refined_deg 1.833 r_angle_other_deg 0.938 r_chiral_restr 0.12 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 24768 Nucleic Acid Atoms Solvent Atoms 2470 Heterogen Atoms 297
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing