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Crystal structure of ethanolamine ammonia-lyase from Escherichia coli complexed with CN-Cbl and ethanolamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QEZ PDB ENTRY 2QEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 6.0-7.0 % (w/v) PEG 6000, 24-26 % (v/v) glycerol, 5.0 % (v/v) 2-propanol, 0.1 M HEPES-NaOH, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.93 68.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 242.76 α = 90 b = 242.76 β = 90 c = 76.46 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 2008-07-11 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 2.1 50 97.2 0.096 17.9 6.8 145836 145836
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 93.1 4.35 6.3 9228
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 SAD, MR THROUGHOUT PDB ENTRY 2QEZ 2.1 47.51 138458 7304 97.15 0.24099 0.23966 0.2551 0.2663 0.2837 RANDOM 15.448
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 40.009 r_dihedral_angle_4_deg 20.776 r_dihedral_angle_3_deg 19.292 r_dihedral_angle_1_deg 10.632 r_scangle_it 4.809 r_scbond_it 3.371 r_mcangle_it 1.737 r_mcbond_it 1.129 r_angle_refined_deg 0.866 r_chiral_restr 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.009 r_dihedral_angle_4_deg 20.776 r_dihedral_angle_3_deg 19.292 r_dihedral_angle_1_deg 10.632 r_scangle_it 4.809 r_scbond_it 3.371 r_mcangle_it 1.737 r_mcbond_it 1.129 r_angle_refined_deg 0.866 r_chiral_restr 0.26 r_bond_refined_d 0.013 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 707 Heterogen Atoms 222
Software Software Software Name Purpose SHARP phasing PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling