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X-ray crystal structure of the YdjI aldolase from Escherichia coli K12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GVF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 10-12% PEG5000
100 mM MES
5 mM DHAP
Crystal Properties Matthews coefficient Solvent content 2.14 42.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.763 α = 90 b = 85.663 β = 109.88 c = 84.268 γ = 90
Symmetry Space Group P 1 21 1
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 QUANTUM 210r 2018-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.75 50 96.5 0.071 0.071 33.2 3.6 104686
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 90.6 0.213 0.213 4.4 2.6
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 1gvf 1.75 34.74 99486 5200 96.52 0.14342 0.14145 0.1535 0.18156 0.1906 RANDOM 23.881
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] 0.11 0.32 0.33 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 18.299 r_dihedral_angle_3_deg 14.033 r_long_range_B_refined 6.044 r_dihedral_angle_1_deg 6.024 r_long_range_B_other 5.874 r_scangle_other 5.042 r_scbond_it 3.344 r_scbond_other 3.343 r_mcangle_other 2.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.794 r_dihedral_angle_4_deg 18.299 r_dihedral_angle_3_deg 14.033 r_long_range_B_refined 6.044 r_dihedral_angle_1_deg 6.024 r_long_range_B_other 5.874 r_scangle_other 5.042 r_scbond_it 3.344 r_scbond_other 3.343 r_mcangle_other 2.964 r_mcangle_it 2.961 r_mcbond_it 2.101 r_mcbond_other 2.101 r_angle_refined_deg 1.443 r_angle_other_deg 0.491 r_chiral_restr 0.072 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8115 Nucleic Acid Atoms Solvent Atoms 999 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing