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Class II fructose 1,6-bisphosphate aldolase with Cadmium (not Zinc) in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZEN PDB ENTRY 1ZEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.6 pH 7.60
Crystal Properties Matthews coefficient Solvent content 3.22 61.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.331 α = 90 b = 77.331 β = 90 c = 290.851 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE FUJI M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 38.3 86.9 0.057 12.8 2.5 31355
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 2.05 51 0.294 1.3 1.5
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 1ZEN 2 38.35 29766 1580 87.2 0.169 0.168 0.1783 0.193 0.1981 RANDOM 25.16
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.971 r_scangle_it 6.838 r_dihedral_angle_1_deg 5.443 r_scbond_it 4.331 r_mcangle_it 2.771 r_angle_refined_deg 2.56 r_mcbond_it 1.606 r_angle_other_deg 1.243 r_nbtor_other 0.346 r_metal_ion_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.971 r_scangle_it 6.838 r_dihedral_angle_1_deg 5.443 r_scbond_it 4.331 r_mcangle_it 2.771 r_angle_refined_deg 2.56 r_mcbond_it 1.606 r_angle_other_deg 1.243 r_nbtor_other 0.346 r_metal_ion_refined 0.325 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.253 r_nbd_other 0.215 r_symmetry_vdw_other 0.189 r_chiral_restr 0.182 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.114 r_bond_refined_d 0.02 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_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 2538 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling