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Crystal structure of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12 - Mg-pyruvate product complex
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 = 105.6 α = 90 b = 137.7 β = 90 c = 124.1 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 2005-07-10 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 1.93 53 94 0.04 32.2 4.6 63843 -3 31.4
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 1.93 2 95.5 0.34 2.7 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 MAD THROUGHOUT PDB ENTRY 1DXE 1.93 52.7 61264 2579 94 0.169 0.168 0.166 0.206 0.2051 RANDOM 37.47
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] 2.66 -0.98 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.012 r_dihedral_angle_3_deg 14.055 r_dihedral_angle_4_deg 11.714 r_dihedral_angle_1_deg 6.82 r_scangle_it 3.183 r_scbond_it 2.163 r_angle_refined_deg 1.475 r_mcangle_it 1.416 r_mcbond_it 0.912 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.012 r_dihedral_angle_3_deg 14.055 r_dihedral_angle_4_deg 11.714 r_dihedral_angle_1_deg 6.82 r_scangle_it 3.183 r_scbond_it 2.163 r_angle_refined_deg 1.475 r_mcangle_it 1.416 r_mcbond_it 0.912 r_nbtor_refined 0.304 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.165 r_symmetry_hbond_refined 0.128 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 543 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing