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Crystal structure of ethanolamine ammonia-lyase from escherichia coli complexed with CN-CBL and (R)-2-amino-1-propanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABR PDB ENTRY 3ABR
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 4.23 70.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 244.073 α = 90 b = 244.073 β = 90 c = 76.98 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 IMAGE PLATE BRUCKER DIP-6040 MIRRORS 2008-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU SPring-8 BL44XU
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 2.1 48 92.9 0.087 13.2 3.3 141897 141897
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 2.1 2.15 91.5 0.443 2.99 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 3ABR 2.1 47.84 134843 134843 7043 92.79 0.248 0.248 0.246 0.2601 0.276 0.2909 RANDOM 43.579
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] 0.28 0.14 0.28 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.452 r_dihedral_angle_4_deg 19.673 r_dihedral_angle_3_deg 19.312 r_dihedral_angle_1_deg 9.396 r_scangle_it 4 r_scbond_it 2.745 r_mcangle_it 1.419 r_mcbond_it 0.892 r_angle_refined_deg 0.83 r_chiral_restr 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.452 r_dihedral_angle_4_deg 19.673 r_dihedral_angle_3_deg 19.312 r_dihedral_angle_1_deg 9.396 r_scangle_it 4 r_scbond_it 2.745 r_mcangle_it 1.419 r_mcbond_it 0.892 r_angle_refined_deg 0.83 r_chiral_restr 0.22 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 711 Heterogen Atoms 192
Software Software Software Name Purpose BSS data collection REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling