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Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and 2-amino-1-propanol
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.M imidazole-HCl, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.9 68.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 241.87 α = 90 b = 241.87 β = 90 c = 76.29 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 RIGAKU JUPITER 210 mirrors 2009-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
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 2.05 50 99.5 0.079 18.9 5.2 158931 158931
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 2.05 2.1 94.6 0.463 2.55 3.4 10007
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 2.05 50 150949 7958 99.45 0.23173 0.2298 0.2551 0.26861 0.2896 RANDOM 13.083
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] -0.73 -0.37 -0.73 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_4_deg 15.373 r_dihedral_angle_3_deg 14.488 r_scangle_it 7.231 r_dihedral_angle_1_deg 6.376 r_scbond_it 5.938 r_mcangle_it 3.567 r_mcbond_it 2.767 r_angle_refined_deg 0.989 r_chiral_restr 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.032 r_dihedral_angle_4_deg 15.373 r_dihedral_angle_3_deg 14.488 r_scangle_it 7.231 r_dihedral_angle_1_deg 6.376 r_scbond_it 5.938 r_mcangle_it 3.567 r_mcbond_it 2.767 r_angle_refined_deg 0.989 r_chiral_restr 0.217 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 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 10735 Nucleic Acid Atoms Solvent Atoms 1010 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling