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Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DXE PDB ENTRY 1DXE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 WRIGHT, A., BLEWETT, A., FULOP, V., COOPER, R., BURROWS, S., JONES, C. & ROPER, D. (2002). EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CHARACTERIZATION OF AN HHED ALDOLASE HOMOLOGUE FROM ESCHERICHIA COLI K12. ACTA CRYST. D58, 2191-2193., pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.5 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.2 α = 90 b = 136.8 β = 90 c = 123.2 γ = 90
Symmetry Space Group C 2 2 21
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 CCD MIRRORS 2002-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 1.39 60 99.5 0.06 27.2 4.3 176395 -3 18.8
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 1.39 1.44 99.3 0.4 2.1 3.3
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 ENTRY 1DXE 1.39 59.76 169354 7041 99.5 0.172 0.171 0.1713 0.191 0.19 RANDOM 23.74
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] 0.62 -0.1 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.943 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_4_deg 10.941 r_dihedral_angle_1_deg 5.848 r_scangle_it 3.635 r_scbond_it 2.437 r_mcangle_it 1.672 r_angle_refined_deg 1.599 r_mcbond_it 1.12 r_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.943 r_dihedral_angle_3_deg 12.867 r_dihedral_angle_4_deg 10.941 r_dihedral_angle_1_deg 5.848 r_scangle_it 3.635 r_scbond_it 2.437 r_mcangle_it 1.672 r_angle_refined_deg 1.599 r_mcbond_it 1.12 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.107 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5853 Nucleic Acid Atoms Solvent Atoms 959 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing