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x-ray structure of NeoB from streptomyces fradiae in complex with PLP and neomycin (as the external aldimine) at pH 7.5
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 18-20% PEG-5000, 200 mL LiCl, 100 mM HEPES, 1 mm PLP, 5 mM neomycin
Crystal Properties Matthews coefficient Solvent content 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.255 α = 90 b = 109.576 β = 110.5 c = 70.443 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 Bruker Platinum 135 2017-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 1.35 50 98.7 0.075 0.075 10.9 5.2 181651
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 1.35 1.45 96.1 0.393 0.393 2.4 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6cbk 1.35 50 172422 9229 98.71 0.17284 0.17157 0.19681 0.1966 RANDOM 15.11
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] 0.15 -0.21 0.37 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.817 r_dihedral_angle_4_deg 16.032 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 6.206 r_long_range_B_refined 5.823 r_long_range_B_other 5.823 r_scangle_other 4.356 r_scbond_it 2.95 r_scbond_other 2.948 r_mcangle_other 2.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.817 r_dihedral_angle_4_deg 16.032 r_dihedral_angle_3_deg 13.508 r_dihedral_angle_1_deg 6.206 r_long_range_B_refined 5.823 r_long_range_B_other 5.823 r_scangle_other 4.356 r_scbond_it 2.95 r_scbond_other 2.948 r_mcangle_other 2.23 r_mcangle_it 2.229 r_mcbond_it 1.694 r_angle_refined_deg 1.693 r_mcbond_other 1.656 r_angle_other_deg 0.847 r_chiral_restr 0.11 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 6188 Nucleic Acid Atoms Solvent Atoms 953 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing