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Complex of bifunctional aldos-2-ulose dehydratase with the reaction intermediate ascopyrone M
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A7K PDB ENTRY 4A7K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1 M BISTRIS-PROPANE, 0.2 M NACL, 16% PEG6000. CRYSTALS WERE OBTAINED BY CO-CRYSTALLISATION IN THE PRESENCE OF 0.2 M ANHYDROFRUCTOSE INCUBATED WITH 0,2M HYDROXYLAMINE, pH 7
Crystal Properties Matthews coefficient Solvent content 2.71 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.22 α = 90 b = 82.67 β = 90 c = 97.91 γ = 90
Symmetry Space Group P 21 21 2
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.6 42 93.2 0.12 8.4 4 33047
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 2.6 2.7 99.3 0.54 2.2 3.6
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 PDB ENTRY 4A7K 2.6 41.33 31351 1674 97.94 0.19739 0.19376 0.1935 0.26694 0.2679 RANDOM 35.558
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] -0.56 1.61 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_4_deg 20.189 r_dihedral_angle_3_deg 16.982 r_dihedral_angle_1_deg 7.193 r_angle_refined_deg 1.695 r_chiral_restr 0.107 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.655 r_dihedral_angle_4_deg 20.189 r_dihedral_angle_3_deg 16.982 r_dihedral_angle_1_deg 7.193 r_angle_refined_deg 1.695 r_chiral_restr 0.107 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_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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 6801 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing