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Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with adeninylpentylcobalamin and ethanolamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABO PDB ID 3ABO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 277 6.0-7.0% (w/v) PEG 4000, 24-26% (v/v) glycerol, 1.0 % (v/v) 2-methyl-2,4-pentanediol (MPD), 0.1M imidazole-HCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.94 68.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 242.73 α = 90 b = 242.73 β = 90 c = 76.66 γ = 120
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 270 mirrors 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 2.25 50 98.3 0.101 21.9 9.6 120002 120002
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 2.25 2.3 85 0.516 2.47 4.4 6841
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 PDB ID 3ABO 2.25 50 113966 6020 98.23 0.21533 0.21378 0.2319 0.24439 0.2468 RANDOM 20.25
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] -0.51 -0.25 -0.51 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_4_deg 16.47 r_dihedral_angle_3_deg 14.899 r_scangle_it 8.279 r_scbond_it 5.984 r_dihedral_angle_1_deg 5.111 r_mcangle_it 2.402 r_mcbond_it 1.543 r_angle_refined_deg 1.187 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.247 r_dihedral_angle_4_deg 16.47 r_dihedral_angle_3_deg 14.899 r_scangle_it 8.279 r_scbond_it 5.984 r_dihedral_angle_1_deg 5.111 r_mcangle_it 2.402 r_mcbond_it 1.543 r_angle_refined_deg 1.187 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10760 Nucleic Acid Atoms Solvent Atoms 660 Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling