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Structure of an Archaeal fructose-1,6-bisphosphate aldolase with the catalytic Lys covalently bound to the carbinolamine intermediate of the substrate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OJX PDB ENTRY 1OJX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 9% (W/V) PEG 4000, 0.1 M NAACETATE PH 5.0, 1-8% GLYCEROL, 100 MM FBP
Crystal Properties Matthews coefficient Solvent content 2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.9 α = 90 b = 159.2 β = 107.8 c = 101.4 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 MARRESEARCH 2003-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 40 97.3 0.08 16.2 4.2 179009 -3
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 2.02 77.6 0.37 2.2 2.5
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 1OJX 1.93 39.8 179009 2723 100 0.15654 0.15592 0.1574 0.19811 0.1984 RANDOM 22.83
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] -0.02 -0.06 0.06 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 19.855 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 5.722 r_scangle_it 3.395 r_scbond_it 2.158 r_angle_refined_deg 1.485 r_mcangle_it 1.125 r_mcbond_it 0.657 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.892 r_dihedral_angle_4_deg 19.855 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_1_deg 5.722 r_scangle_it 3.395 r_scbond_it 2.158 r_angle_refined_deg 1.485 r_mcangle_it 1.125 r_mcbond_it 0.657 r_chiral_restr 0.109 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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_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 19381 Nucleic Acid Atoms Solvent Atoms 1518 Heterogen Atoms 200
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing