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Structural of ABDH, a beta-diketone hydrolase from the Cyanobacterium Anabaena sp. PCC 7120 bound to (S)-3-oxocyclohexyl acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O8U PDB ENTRY 1O8U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1 M BIS-TRIS PROPANE PH 7.5, 20% PEG 3350, 0.2 M SODIUM MALONATE, 0.01 M BICYCLO[2.2.2]OCTANE-2,6-DIONE
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.387 α = 90 b = 80.387 β = 90 c = 125.882 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 ADSC CCD TOROIDAL MIRROR 2006-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.57 40.19 98.9 0.06 32.04 10.1 64435
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 1.57 1.63 89.9 0.27 2.93 4.8
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 1O8U 1.57 40.19 60411 3228 98.8 0.14 0.138 0.1371 0.17 0.1702 RANDOM 14.19
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] 0.49 0.25 0.49 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.768 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_3_deg 11.806 r_dihedral_angle_1_deg 5.986 r_scangle_it 2.542 r_scbond_it 1.755 r_angle_refined_deg 1.518 r_mcangle_it 1.146 r_mcbond_it 0.792 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.768 r_dihedral_angle_4_deg 14.64 r_dihedral_angle_3_deg 11.806 r_dihedral_angle_1_deg 5.986 r_scangle_it 2.542 r_scbond_it 1.755 r_angle_refined_deg 1.518 r_mcangle_it 1.146 r_mcbond_it 0.792 r_nbtor_refined 0.317 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.156 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 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 4016 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing