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Crystal structure of 2-dehydro-3-deoxyphosphooctonate aldolase from Vibrio cholerae O1 biovar eltor str. N16961
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O60
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 291 0.05 Ammonium sulfate
0.05 bis-tris
30% pentaerythritol ethoxylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.187 α = 90 b = 117.187 β = 90 c = 117.187 γ = 90
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 SBC-3 MIRRORS 2008-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 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 1.8 40 99.9 0.082 0.78 40 20.3 24922 28.4
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 1.8 1.83 100 0.78 1.9 19.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 1O60 1.8 40 23054 23054 1245 97.5 0.178 0.176 0.1815 0.215 0.2198 RANDOM 16.59
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_4_deg 21.548 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.059 r_scangle_it 3.462 r_scbond_it 2.507 r_angle_refined_deg 1.726 r_mcangle_it 1.499 r_mcbond_it 1.256 r_angle_other_deg 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.98 r_dihedral_angle_4_deg 21.548 r_dihedral_angle_3_deg 13.827 r_dihedral_angle_1_deg 6.059 r_scangle_it 3.462 r_scbond_it 2.507 r_angle_refined_deg 1.726 r_mcangle_it 1.499 r_mcbond_it 1.256 r_angle_other_deg 1 r_mcbond_other 0.347 r_symmetry_hbond_refined 0.313 r_symmetry_vdw_other 0.238 r_nbd_refined 0.221 r_nbd_other 0.197 r_symmetry_vdw_refined 0.196 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.111 r_nbtor_other 0.089 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2108 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing CCP4 phasing