☰ Navigation Tabs
Structure of the Class II Fructose-1,6-Bisphophatase from Francisella tularensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 20 mM Tricine pH 7.8, 50 mM KCl, 1 mM MgCl2,
0.1 mM DTT, 15% glycerol;
Composition of reservoir solution 0.2 M sodium formate, 20% PEG 3350;
Volume and ratio of drop 22.4 uL (1:1)
Volume of reservoir (ul) 100
Crystal Properties Matthews coefficient Solvent content 2.4 51.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.296 α = 90 b = 100.169 β = 90.003 c = 92.021 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 MARMOSAIC 300 mm CCD 2017-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.92456 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) CC (Half) 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 2.4 40 98.9 0.106 0.106 0.991 24.6 3.6 53682 1 1 42.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 97.5 0.531 0.531 0.531 0.276 0.673 3.2 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 6ayu 2.4 38.11 1 53662 2732 98.747 0.155 0.1534 0.1532 0.193 0.1927 2732 48.033
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] -5.067 -3.658 -0.204 5.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.764 r_dihedral_angle_3_deg 19.094 r_dihedral_angle_4_deg 17.373 r_dihedral_angle_1_deg 13.49 r_lrange_it 7.692 r_lrange_other 7.692 r_scangle_it 5.503 r_scangle_other 5.503 r_mcangle_it 5.429 r_mcangle_other 5.429
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.764 r_dihedral_angle_3_deg 19.094 r_dihedral_angle_4_deg 17.373 r_dihedral_angle_1_deg 13.49 r_lrange_it 7.692 r_lrange_other 7.692 r_scangle_it 5.503 r_scangle_other 5.503 r_mcangle_it 5.429 r_mcangle_other 5.429 r_scbond_it 3.873 r_scbond_other 3.873 r_mcbond_it 3.747 r_mcbond_other 3.746 r_angle_other_deg 1.605 r_angle_refined_deg 1.5 r_nbd_other 0.343 r_symmetry_nbd_refined 0.278 r_xyhbond_nbd_refined 0.248 r_symmetry_nbd_other 0.232 r_symmetry_xyhbond_nbd_refined 0.219 r_nbd_refined 0.208 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_other 0.138 r_symmetry_metal_ion_refined 0.102 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.068 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9624 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing