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2.1 Angstrom X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale SB4, with Michaelis analog (L-alpha-lysine external aldimine form of pyridoxal-5'-phosphate).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 300 sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K 2 VAPOR DIFFUSION, HANGING DROP 8 300 sodium N-2-hydroxy-ethylpiperazine-N'--3-propage sulfonic acid (EPPS, or HEPPS), sodium malonaate, L-alpha-lysine, dithiothreitol, polyethylene glycol 200, polyethylene glycol 8000, s-adenosylmethionine, iron-II-sulfate, , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.89 α = 90 b = 92.926 β = 96.74 c = 177.735 γ = 90
Symmetry Space Group C 1 2 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 315 monochromator with Si (111) crystal 2003-04-09 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD ADSC QUANTUM 4 monochromator with Si(111) double-crystal 2003-03-28 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9742 NSLS X25 2 SYNCHROTRON APS BEAMLINE 17-ID 0.9792 APS 17-ID
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 1,2 2.1 50 81.53 0.103 0.103 2 3 83957 83957
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) 1,2 2.1 2.18 62.3 0.265 0.265 2.97 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 2.1 50 83957 83957 7437 81.53 0.18732 0.18396 0.2661 0.22485 0.2922 RANDOM 33.824
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] 0.3 -1.71 3.3 -4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.993 r_dihedral_angle_4_deg 20.774 r_dihedral_angle_3_deg 20.343 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 3.086 r_scangle_it 2.362 r_scbond_it 1.635 r_mcangle_it 0.861 r_mcbond_it 0.582 r_symmetry_hbond_refined 0.393
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.993 r_dihedral_angle_4_deg 20.774 r_dihedral_angle_3_deg 20.343 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 3.086 r_scangle_it 2.362 r_scbond_it 1.635 r_mcangle_it 0.861 r_mcbond_it 0.582 r_symmetry_hbond_refined 0.393 r_symmetry_vdw_refined 0.382 r_nbtor_refined 0.317 r_nbd_refined 0.232 r_chiral_restr 0.177 r_xyhbond_nbd_refined 0.164 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12990 Nucleic Acid Atoms Solvent Atoms 608 Heterogen Atoms 264
Software Software Software Name Purpose REFMAC refinement CBASS data collection MX data reduction JBluIce-EPICS data collection SCALEPACK data scaling SOLVE phasing