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X-ray structure of GenB1 from micromonospora echinospora in complex with neamine and PLP (as the external aldimine)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 17-19% PEG-8000, 2% 2-propanol, 1 mM PLP, 5 mM neamine, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.32 47.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.888 α = 90 b = 59.98 β = 95.19 c = 210.694 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 92.3 0.048 0.048 36.4 2.7 201237
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 83.4 0.111 0.111 10.5 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.6 50 191197 10040 92.16 0.15685 0.15521 0.1682 0.18818 0.1979 RANDOM 17.067
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] -0.66 -0.19 1.46 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.754 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 14.206 r_long_range_B_refined 6.043 r_long_range_B_other 6.043 r_dihedral_angle_1_deg 5.99 r_scangle_other 4.502 r_scbond_it 3.007 r_scbond_other 2.999 r_mcangle_other 2.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.754 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 14.206 r_long_range_B_refined 6.043 r_long_range_B_other 6.043 r_dihedral_angle_1_deg 5.99 r_scangle_other 4.502 r_scbond_it 3.007 r_scbond_other 2.999 r_mcangle_other 2.421 r_mcangle_it 2.42 r_mcbond_it 1.765 r_mcbond_other 1.763 r_angle_refined_deg 1.735 r_angle_other_deg 0.897 r_chiral_restr 0.167 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 12436 Nucleic Acid Atoms Solvent Atoms 1614 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing